I really don't mind if the TNG/DS9 logo's are retired and its all viewed as part of one continuity.
I don't see any reason to retire them. It's fine to leave them out for books that aren't specific to any one series, but a lot of the 24th-century books still are very much linked to a single specific series. Cold Equations
, for example, was unambiguously a TNG trilogy, not a generic Trek trilogy.