My phone doesn't have an SD card in it right now, so all storage is on internal memory. I have a bunch of folders in my Pictures folder that don't show up on my PC when I connect it via USB (but most folders do appear). I know they're there because they appear in my phone's file manager (in both the native Google one and a third-party one). How come I can't see them?
This is a known issue. Go to app manager and find 'external storage' and 'media storage' and clear data and cache for them, then reboot, and wait up to 10 minutes and then connect to PC via USB. Sometimes media scan apps from play store help if you don't want to reboot.
I find another trick that works on Android 8.1, not sure other versions, that you can reboot your phone to recovery mode, specifically I installed TWRP, then the missing folders show up on my computer.
Note, for Android OS developers, if you just flashed the system image, you have to at least boot into desktop once, the computer then can recognize the phone under recovery mode.