Is it suggested to leave them in or to remove them when storing for long periods? Does it harm it at all or is it just more convenient to leave them in? Does leaving them in drain the battery after many years?
Probably a non issue.
The drain is minimal.
If the battery should fail, they are cheap to replace.
The default bios settings will be available.
Probably more convenient to keep it in the motherboard so you don't lose the battery.