A secret lair is dwelling place of darker evils.
It's secret, as opposed to "well known", because these evils are doing all sorts of nasty things they don't want anyone else to know about. Also, if they need to kidnap a hero's SO or flee to their lair to nurse their wounds, it's better to have it located somewhere secret and inaccessible, so they can't be easily pursued by our brave hero.
It's a lair because, for instance, a secret phone booth or deviously hidden infinitely large star lacks many of the advantages of a lair. One can neither nurse their wounds nor hoard treasure in a phone booth. It is also rather useless for building doomsday machinery capable of conquering the earth.
Some villains, particularly the "mad, and twisted, but human" types (as opposed to the "ancient and dark, very evil" types) have a secret castle rather than a secret lair. All a matter of preference, really.
The good guys have a secret hideout or secret fortress. Never a lair. It accomplishes the same (albeit good rather than evil) purposes as a lair, but it is not a lair.
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