How can I patch holes in the roof left by satellite dish removal?
Leaving the lag bolts in is fine, but the bolts are likely made out of galvanized steel, meaning they will rust and corrode eventually when exposed to constant rain and water.  It is best to liberally apply roof cement patch to the lag bolts to ensure that no water will corrode or leak through where the bolts are.

You can get roof cement patch in a tube form like so that easily fits into a standard caulking gun.



It will eventually wear away so I would check on the patches every 3 or 4 years to make sure they are still there.