I have done it in Geneforge 3 and Geneforge 4. In Geneforge 3, it improves the ending slightly if you play a Shaper loyalist, but using them is helpful and it doesn't hurt your ending much. In Geneforge 4, the good Shaper ending is only possible if you use less than 7 canisters, and using canisters in that game makes some fights impossible to avoid as they cause insanity(which is part of why the Shapers forbid their use.) I have never tried going canister free in Geneforge 2, and the other two Geneforge games do not change whether you use canisters or not.