It depends how it is used. Can you give a full example?
Is indepth analysis hyphenated?
It is never one word: there is no such English as "indepth." But you should definitely separate the words "in depth," or more commonly, put a hyphen between them: "in-depth analysis." This is probably more correct because "in-depth" is a compound adjective (this occurs when two words are put together with a hyphen to form an adjective; other examples are "well-deserved" and "long-awaited").
Should there be a hyphen after finger and toe when writing finger and toenails?
No there shouldn't be a hyphen. Fingernails and toenails are full words.
Look for loose plastic trim around the exterior edge of you windshield. For years, I would get a wind rattle at 50 mph whenever I was next to a big rig. The noise came straight through the center vent. Something about the physics of aerodynamics would lift the plastic trim at the base of the windshield. After a 50 cent plastic rivet, the wind rattle was gone. Another thing to check are the rubber jack points under the sills. if one or more of these are missing the wind will enter the body at this point and appear as wind noise at the windscreen. I had this problem and confirmed this by using tape to cover over the hole and went for a spin down the motorway. that's the cheap fix, the rubber mounts from BMW were a bit too expensive for me.
No, hardly ever.
Sometimes words that would have a double e might be hyphenated, like re-elect just to make them easier to read (reelect).