"Was the world (and I guess therefore the universe as well) perfect in the beginning? Didn't it suffer from any natural disasters such as earthquakes, tornadoes, storms...?".
Let's unpack your sentence, above, before we attempt to answer your question.
First, biblically speaking the world and the universe were never perfect. The word perfection is reserved for a thrice-holy God. Perfection in this sense is not only the absence of imperfection; it is also the presence of impossible-to-perfect attributes, such as holiness, for example. God can never get better (the comparative of good!) than He is, was, or ever will be.
"'I the LORD do not change. So you, O descendants of Jacob, are not destroyed. Ever since the time of your forefathers you have turned away from my decrees and have not kept them. Return to me, and I will return to you,' says the LORD Almighty" (Malachi 3:6 NIV).
In other words, when God created the material universe, He declared it to be only good, not perfect. Big difference!
Second, as to "natural disasters," I have to disagree with LCIII, above, when he suggests that tornadoes and storms are "just . . . weather." I'm almost fully convinced that natural disasters (from a human perspective, particularly when lives are lost and property is destroyed) were not a part of God's original plan for Planet Earth.
While the creation, Paul reminds us in Romans 8, was "subjected to futility" (v.20), this futility did not appear instantly the moment our first parents sinned. I suggest the whole gamut of natural disasters may have taken centuries to appear on our favored planet. In fact, I suggest that the disasters we call natural (which are in a sense unnatural because of the fall of humankind) did not appear until after the worldwide flood with which God punished all the inhabitants of the world, save the eight people of Noah's family.
Is there biblical proof for what I have just suggested? Probably not. I'll venture to guess, however, that natural conditions in the antediluvian world compared to the post-diluvian world, were radically changed. To this day, we cannot imagine how radical those changes may have been, given the world was completed deluged with water. The Bible tells us plainly,
"the waters . . . increased greatly . . . and the mountains were covered" (Genesis 7:18-20).
It also tells us,
"In the six hundredth year of Noah's life, in the second month, the seventeenth day of the month, the same day were all the fountains of the great deep broken up , and the windows of heaven were opened" (Genesis 7:11 KJV).
This suggests to me that with that amount of water covering the entire earth, the entire "balance" (for want of a better word) in nature was changed forever (well, until God creates a "new heaven and a new earth," Revelation 21:1 KJV). In short, the flood, I suggest, was responsible for natural disasters. Is it possible that even the axis of the earth was changed because of the worldwide flood? Perhaps. The Bible does tell us that
"The world that then was, being overflowed with water, perished" (2 Peter 3:6).
Dr. John Morris suggests
"[The pre-flood earth was] gone forever. The earth of today was radically altered by that global event."
Dr. Morris goes on to say (and forgive me for the extensive quotation, but I think it serves to underscore the radical changes which occurred in the post-diluvian world),
That Flood accomplished abundant geologic work. Eroding sediments here, redepositing them there, pushing up continents, elevating plateaus, denuding terrains, etc., so that the earth today is quite different from before. Today even mountain ranges rise high above the sea.
Mt. Everest and the Himalayan range, along with the Alps, the Rockies, the Appalachians, the Andes, and most of the world's other mountains are composed of ocean-bottom sediments, full of marine fossils laid down by the Flood. Mt. Everest itself has clam fossils at its summit. These rock layers cover an extensive area, including much of Asia. They give every indication of resulting from cataclysmic water processes. These are the kinds of deposits we would expect to result from the worldwide, world-destroying Flood of Noah's day.
At the end of the Flood, after thick sequences of sediments had accumulated, the Indian subcontinent evidently collided with Asia, crumpling the sediments into mountains. Today they stand as giants—folded and fractured layers of ocean-bottom sediments at high elevations. No, Noah's Flood didn't cover the Himalayas, it formed them!
While God did indeed punish the hopelessly corrupt peoples of the earth in Noah's day (see, for example, Genesis 6:5-8), His judgment radically affected the planet on which the flood was visited. Furthermore, I believe that God is not going to reverse those effects, which we experience today as tornadoes, hurricanes, tsunamis, earthquakes, and more, until He brings history to a close and usher in a new heaven and a new earth.
Does God "make" natural disasters occur? Perhaps a better expression would be "God allows natural disasters to take place" for His own purposes. To attempt to "figure out" what those purposes might be is indeed a futile undertaking. Each disaster in which human life is lost is a tragedy. To think that God is unconcerned with the effect of these disasters on us who were created in His image is ludicrous.
Are these disasters, therefore, always punishments from God on those whose lives are lost and homes and property destroyed? I don't think so. Occasionally they may in fact be a severe form of divine discipline and punishment, but even in the perhaps rare instances in which they are divine punishment, God's design is always with the overall purpose of turning people's eyes from the material world, which is in the process of decay and destruction, to spiritual verities and realities which cannot be corrupted or destroyed (see Matthew 6:20).
That is one reason why the church universal should be "first responders" to natural disasters. Local churches in the vicinity of the disaster should be the first to offer help, hope, and healing in Jesus' name. They should be among the first to demonstrate the love of God in practical ways, to the end that people will come to know the only truly secure possession which can never be destroyed, and that is eternal life through Christ our Lord.
Put differently, and in conclusion, there is something more important and significant than temporal life, and that is eternal life. Moreover, we have the assurance of God's word that
". . . the creation itself also will be set free from its slavery to corruption into the freedom of the glory of the children of God. For we know that the whole creation groans and suffers the pains of childbirth together until now. And . . . also we ourselves . . . [wait] eagerly for our adoption as sons, the redemption of our body. For in hope we have been saved, but hope that is seen is not hope; for who hopes for what he already sees? But if we hope for what we do not see, with perseverance we wait eagerly for it" (Romans 8:21-25, excerpts, NASB, UV).