How to patch holes in the roof left by satellite dish removal

I wouldn't worry too much about it. The plywood is not typically supporting a load of more than the paper and asphalt shingles that were placed, even more so if you have a considerable pitch on your roof to where it would be difficult or impossible for a person to walk on. It basically serves so that you have something to nail the shingles down securely.

Most newer homes use plywood, I have an older home that used what looks like rough cut deck planks and those are mostly still original. The last time I had my roof replaced, they had to change out a few boards that were terribly dry rotted and some that were badly damaged from previous water damage by the oh-so responsible homeowners who had the home before me. Other older boards look noticeably damaged by the most recent nails but they continue to hold down the shingles and I would still feel safe to stand on my roof.

As long as the shingles are doing their job then the plywood will not be exposed to any water, and as long as your attic has good ventilation during the summer time then you should have nothing to worry about for the next 15-20 years at least.

Here is what I ended up doing:

The entire roof had an ice and water shield that was sticking the shingles. This guy's write-up about his roof closely mirrors my situation in that it was south facing, low slope, and old.

After deciding to just lay shingles onto the remaining old shingles, I noticed that the sun warmed up the substance to the point where it was relatively easy to peel off the stuck shingles with the roofer's spade. So I got the old shingles off, put down felt and applied new roof. Thanks!