Okay, so I started the game and imported what I thought was all my content from LBP and LBP2 (turned out to be only my profile from LBP). I played through the game and went on creator and realized that I didn't have any of my LBP2 stuff. So, I backed up my LBP2 profile and imported it into LBP3 and realized that all of the collectibles had reset which was kinda annoying (none of the upgrades had reset though). So, I started the game again to get the collectibles again and found out that when in the HUB areas (I checked all 3 and it was the same) that there were no collectibles or collectibells anywhere, despite the level saying that there were still all the items to collect. Is this a glitch or just something unavoidable when playing the game on a different profile?

It's a glitch. Many others are experiencing this glitch. I have this strange glitch where Zom Zom doesn't show up if you near the level link to his store like he usually does, but you can still hear his dialogue.

This glitch might be more fatal than mine, though. You might still be able to get the costumes from Zom Zom's shop by starting LBP3 on a different user (let's call this "User 2", collecting the collect-a-bells on that user, entering Zom Zom's shop, then turning on a second controller to spawn your main user (the one with the glitch). When the collect-a-bells of User 2 are used to buy the costumes in Zom Zom's shop, User 2 or your main user can collect the prize bubbles and its contents will be shared with both players, which means that you'll have those costumes on your main account. Nifty trick if you ask me.