Internal storage management of files and folders
Without a list of your internal storage content, it's hard to discern useless files from useful ones. Without further info, the only answers I can give you are the following:


When you uninstall an app, the system deletes the trees corresponding to the app's package name under /data/app/ (application executable) and /data/data/ (application's internal data). It should also wipe some folders into your internal and external storages, namely those corresponding to the app's package name, and placed under Android/data/. Any other folder, created by the app in a path different from the abovementioned gets ignored.
It may depend. Generally, those which slow down badly your device are files which are big in size. Since, as already said, they're not cleaned by the system, that's a burden that falls on you, the user.


As a footnote, the files residing in an internal storage are not fundamental (and I remark that I'm talking about files, not folders). Generally, they can be files which are placed there by an app for the purpose of flag, meaning that said app looks if such file is present, and performs something. Else, it does something else.

Finally, if you delete any of these files, they may be regenerated, if the app that created them is still installed.