I can offer some answers based on my experience playing as Ming:
1. As mentioned, sea borders do not count for mandate maintenance. However, if you share a land border with a giant blob, no matter how small the border is (could be just one province), it can tank your mandate very quickly unless you subjugate that blob into a tributary. Also, land borders of other countries with your colonial nations does not count for mandate maintenance, so you don't need to worry about them.
2. The bonuses are relatively minor, but then again they are also not very difficult to pass (it gets easier over time too, once you completely surround yourself with tributaries and have all your states experiencing prosperity). That said, with the increased costs as per patch 1.23, I recommend to pass them only when you have 100 mandate.
3. I have yet to play as Japan post-Mandate of Heaven, so I'm afraid I cannot offer much advice for them. The shogun would still defend his daimyos from foreign invasion though, as far as I can tell.
4. Confucian subjects are very annoying to say the least. They rarely harmonise, and if they do they never accept wrong cultures. The only reason to keep a Confucian vassal if you want to feed it territories is to let them core the provinces for you (ie, the same as any other vassals). But you will have to manually convert the provinces for them, which kinds of defeats the purpose of having them.