The key to running Gumshoe (even the earliest instances of it) is to simply treat the investigation skills like ones you roll, but you always automatically succeed, so you don't roll.
So when a player describes her character searching the book shelves for books that don't belong, you don't roll "perception" or "spot hidden" or whatever. You just describe what she finds without breaking out of the narrative and using the system.
Then, on top of that, if the player feels there is something more they could learn, they may want to spend a point. When they do, you give them something worth the point. Or, at the very, very worst, you decline the spend, give them something more for free and then tell them there's nothing worth spending a point on here.
It's definitely a matter of scenario design. They now have these planning sheets where you make sure you have enough clues of different skill types and have your bases covered when it comes to point spending.