Was thinking on buying this game again because of sale, but want to know - is the endless enemy waves still in the story-important missions?

They're pretty much there in all the missions AFAIR. It wouldn't make any sense for these not to be there - not only would it make the game much easier than it already is, you're supposed to be a bunch of spies infiltrating deep in enemy territory.

That said, it's now possible to mod the game - one of the things that can be modded is how many turns before reinforcements show up, so I guess it would be possible to either make that a really big number or disable them altogether.

Thanks.