Installing KSP mods by hand without CKAN

Check the mod actually supports your game version too. Most current stuff targets 1.12.x, and an old mod for an older version can load fine and then break saves later. If the readme doesn't say, look at when it was last updated.

Mostly yes. Open the zip and there's usually a GameData folder inside. Copy what's IN that folder into your game's GameData, so you don't end up with GameData/GameData, which is the classic way to make a mod silently not load. Dependencies are listed on the mod's forum thread or readme. ModuleManager is the common one, and that's just a single dll dropped straight into GameData. Some mods ship their dependencies in the zip already, so check before you download extras. CKAN usually spots the hand-installed dll and lists it as auto-detected, so it won't fight you.