[Kalimac]

I think it's more a question of perspective; from the point of view of Bilbo during his adventure (as well by the standards of 99% of the earth's population) an encounter with giant flesh-eating spiders in Mirkwood was a Great Adventure with capital letters. They were a real menace, to say the least, and any sensible mapmaker would be put "there are spiders" on his map as a sort of warning direction, rather like a medieval mapmaker writing "Here be dragons" albeit with considerably more justification.

That was "The Hobbit." In LOTR, none of the characters came within range of the spiders of Mirkwood, and though they doubtless knew of their existence, their importance probably seemed pretty negligible compared to say, the immediate threats you were facing while trudging up Sauron's Road, or the implications of seeing your former comrades' heads being catapulted into your besieged native city. And Shelob, of course, was enough to worry about without pausing to say "D'ye know, Mr. Frodo, I've been thinking that she-creature might have something to do with those nasty spiders as Mr. Bilbo talked about in his book." There was no point in talking about some distance menace when they had plenty of immediate ones.

As for why the spiders are mentioned in the Appendices, it's likely just because the spiders, while nasty, didn't really contribute much to any historical developments or tales. There isn't really much to say about them except "Yes, they're there. Try to avoid them if you can." Shelob had more legend surrounding her, but her children didn't seem to be so interested in that sort of thing. They were more for just waylaying and killing hapless travelers, and probably just never happened to get anyone sufficiently importantly to get themselves into the legends.