Most big budget franchise movies are kinda geared for a trilogy these days anyway. A three-picture deal is almost standard, but it depends on how financially successful the first one is before a sequel is officially given a greenlight by the studio. The contract just ensures that the cast will be available if two more movies are made.
I think Robert Orci did say that the Enterprise sets will not be destroyed after filming is finished, but disassembled and put into storage for possible further use.
Free your mind, and the rest will follow.