Contribution Reports and disabled Financial Types
I'll go with "Yes" and "Often".  This is a long-standing issue that extends beyond financial types and reports.  It's also searches, and almost anything that can be disabled.

An elegant solution might require some thinking through.  My suspicion is that we'll need a new database field to distinguish these two use cases.  You definitely DO want some disabled option values not to be searchable.  I'm not sure if you want to ever not have them appear though.