I was wondering...

Is there an explicit reason that issues that are related to an issue that was fixed upstream are typically not closed yet till the new wheels are released?

For these issues the GEOS fix was released, but the relevant version is not yet in the shapely wheels:
#882, #1069, #1593, #1788, #1789, #1792, #1844, #1870, #1917, #1921, #1932, #2009, #2029, #2090, #2134, #2150, #2170, #2174, #2186?, #2194, #2220

These issues were fixed on GEOS main, but haven't been released yet: #2174

In comparison, issues that are not an upstream issue, but have been resolved in shapely "main" are being closed already at the time the PR is merged, so (also) before releasing the fix/change. An exception that wasn't closed yet: #2137

Wouldn't it be more logical to treat both the same way?

Administration-wise I think the easiest is to close the issues in both cases, and set the "milestone" to the version it will be released is, or the version that well get the correct GEOS version in the wheels... Alternatively, a specific label could be used to mark issues in this situation.