I heard these games had a lot of skills that were just there to be accurate to the source PnP rules, but aren't actually used in game in any meaningful way. Is this true, and if so, which skills are those?

Only a few skills and spells are very important, the game is supposed to be playable with many different parties.
"Ride" and "drive" are useless, many skills have only one or two checks in the whole trilogy, some depend on your playing style. I never used evaluate for example and there's no need to cheat in a tavern if you can get more money with pickpocketing. If you don't want to abuse save/reload for such situations you won't need those skills on the other hand.
Some skills are only needed for one character, some for 2 and some for the whole party.