Indeed. 15 AC vs. 13 AC isn't that much difference in normal circumstances, but with always on Dodge based disadvantage, and typical enemy to-hit bonus ranges, it's a whole world of difference.
For spellcasting and other character abilities sure, and that's a major limitation on many player characters. It ends up being a pretty small part of the overall portfolio in most monster stat blocks though. But yes, against the right enemy it might shut down a key ability. I'm not saying its useless to make your homoculus invisible, I'm just saying that a creature already taking dodge every turn gets substantially less additional defensive utility out of invisibility than other creatures do, and I don't think it would often be worth a half-caster's 2nd level spell slot and concentration.