Is the Trinity considered Homoousios in spirit only or also in matter? We are taught that matter cannot be created nor destroyed. That would be a problem if Jesus was Homoousios physically.
The Bible specifically reveals God as spirit, that is, not physical (John 4:23). So, Jesus took on flesh (the physical dimension), but this was something new. God--the Father, Son, and Spirit0--exist outside of the physical universe. God created the physical universe, so He cannot be inside the physical universe.
So, no, Jesus took on flesh, but neither the Father nor the Spirit did so.
It should also be noted that the law that states matter can be neither created nor destroyed is a natural law and applies to natural things. Obviously, when God created the heavens and the earth, matter was created. This was done supernaturally. So, we have to make sure we apply natural laws only to natural processes and not force them upon God. Jesus certainly was not bound by natural law when He fed the 5,000, raised the dead, healed the blind and many other things.
There's a big difference between "homoousios", which means "same substance", and "homoiousios", which means "similar substance". It was precisely this difference that caused such a ruckus at the Nicene Counsel. Homoousios is the correct term as chosen in the Nicene Creed, and it refers to the spirit, since God is spirit and has not a body like men.
The divine nature of Jesus Christ is homoousios with God the Father and God the Holy Spirit. The human nature of Jesus Christ is fully man, like anyone alive today, only without sin.