So from what I understand a location becomes "cleared" after you have defeated the boss (is this correct?). A location can become uncleared after a certain amount of in-game days (can anyone confirm?). Also, some locations can be cleared and some cannot.

My question is this: Is there a way to differentiate between locations that can be cleared and locations that cannot?

first part, yes, you are correct.

second, there are locations that a) show up on map with a name and b ) are held by a group (Raiders, Gunners, Feral ghouls, Mirelurks, etc). Those can be cleared in most cases.

Yes an area can become cleared after defeating a marked boss.

After being cleared an area can respawn foes.

The reason for respawn can vary.

Sometimes it just respawns after a certain time but doesn't have a marked boss.

Other times it respawns due to a random encounter occurring. (a faction might attack when you are in the area.)

Other times due to a quest being given to clear an area.

There are a few quest areas that don't respawn.

With your second question, i suppose if you play enough you might learn which areas don't become marked as cleared.

i don't pay much attention to that myself as i tend to go to certain places that i know will respawn gear that i require for equipping settlers.