An invisible file is just like any other file except that it can’t be seen in the Finder and aliases to it won’t work. Ditto for an invisible folder. They are generally created by the system or some application or control panel that wants to be sure the user won’t fiddle with them. The ‘Desktop DB’ desktop database file is an example of an invisible system file. Some software creates invisible files; some creates invisible folders. In general it’s hard to tell who’s doing it because the items are invisible. And as long as you continue to use the creator of an invisible item, there’s no problem. But if you stop using it, you may end up with an invisible file that’s just wasting space. Use the Find Invisible Items command in the Cleaning menu to create a list of invisible items which you can then examine to determine if any of them can be deleted. There are options to ignore custom folder icon files and desktop files.
For example, a search for invisible items on my previous computer at work turned up a 10 Mb invisible file formerly used as a disk partition. I deleted it and freed up 10 Mb on my hard disk. Hard disk space is getting cheap, but it’s not that cheap.