The orchestra section of a Scot score serves to designate instrument names for use within the score. This is a matter of convenience, since an orchestra knows instruments only by numbers, not names. If you declare three instruments, such as:
orchestra { flute=1 cello=2 trumpet=3 }
Csound will neither know nor care what you have named the note lists. However, when you use the name $flute, Scot will know you are referring to instr 1 in the orchestra, $cello will refer to instr 2, and $trumpet will be instr 3. You may meaningfully skip numbers or give several instruments the same number. It is up to you to make sure that your orchestra has the correct instruments and that the association between these names and the instruments is what you intend. There is no limit (or a very high one, at least) as to how many instruments you can declare.