Raising minimum iOS Deployment Target Version for App Update
Solution 1:
From my experience those updates just won't show up as available.
When I upgraded OS on my device from 3.1 to 4.1 about 10 available updates appeared immediately in App store app - so that should be the actual behavior.
Solution 2:
In addition to only showing supported updates, the store now offers the "last compatible version". This lets people download an app even if their device doesn't support the most recent version. Unfortunately this means that some people could still download an older version with bugs you have already fixed. There may be a way to disable this, but none of my app updates have introduced new requirements, so I can not test.