I always figured a part of the issue was quality control. Throughout the series, non-replicated food is held to a higher quality and standard compared to replicated food. I always figured it also played a role for other products as well. Even though replicated food solved hunger, food that's actually grown is significantly tastier.
I mean, supposedly, Voyager only had (I think) 53 Photon torpedoes when it arrived in the Delta Quadrant, and they made it sound like they couldn't replace them, even with replicator technology on the ship. Yeah yeah, I know they went through way more than 53 Photon torpedoes in the ship, but I remember it being brought up. I figured a part of the reason was because either A) Photon torpedoes are inherently less reliable, or B) They're unable to replicate some component to the torpedo.