Can spilled coffee cause long term issues to motherboard?

If cleaned properly, water with sugar should not be a problem.

Possible problems after liquid spill:

• A conductive connection between not to be connected parts can occur, leading to random and hard to detect failures.
• If the spilled liquid contains acids or Lyes, this could frett into parts or connection lines. This should not be an issue with coffee, but for example with solder residues.
• If something sticky dries in, dust is likely to collect more easily.
• If water remained between parts it could leed to parasitic capacities that interfere with the regular functions of the board.

For cleaning, water should be sufficient. If you want to play it safe, use distilled water, isopropy alcohol, or a mixture of both.

For drying, it's not that important to get it hot (don't get it too hot, max. 80°C), but to have it long enough in an area of low relative humidity. Hot air can carry more water, which results in a lower relative humidity of the same air sample at higher temperatures. So make sure you have some air exchange when drying. An electric oven on lowest temperature (50°C) and opend door for some hours should do.

As long as you thoroughly dry the motherboard you should be OK. You said you dried it with paper towels, thats good. I would open it back up and have a fan blow on it for a couple hours to make sure all the moisture is gone. As for the sugar, it shouldnt be an issue as it is not conductive.

If you can, rinse the motherboard thoroughly with distilled water, or a dedicated electrical cleaning fluid, this will remove the sugar, but the motherboard must be rinsed well, and then allowed to dry FULLY before being powered up.