Daniel, it is not so clear cut. Most users will not be exposed to a "zoo". Case in point - Open Street Map. In OSM, the entire user base of tens of thousands of people know the meaning of Q123. The "Q" prefix has a strong identity in itself. Anyone will instantly say - yes, it's a Wikidata identifier attached to the majority of important OSM objects. So whenever someone sees an object with the tag "wikidata=Q123" or "brand:wikidata=Q123" or even "species:wikidata=Q123" they know that there is a WD item describing this object, or the brand of this object (e.g. Mc.Donalds store), or the tree species.
As Lydia said, Wikidata is a huge tree in a forest, overshadowing all other trees. It is totally ok for both OSM and some genetics storage to both use the same prefix - there will be no confusion between the users of the two. Yet both of them are likely to reference Wikidata itself. Keeping "Q" as primarily Wikidata identifier will help the users. That's why I call this a philosophical debate - on one hand, there is very real usability problem. On the other, there is a philosophical dilemma - the best approach in a hypothetical world.
Now that we also have Wikibase on OSM wiki, all of the metadata about those tags is also stored in the Q numbers. So "wikidata" key itself is Q827 [1]. Now lets say at some point we decide to store an item's "class" in osm Wiki, e.g. "item_class=Q123". How often do you think users will confuse this Q123 to be wikidata's ID vs OSM wiki ID? This is almost certain to cause confusion, especially among the novice users, without actually benefiting anyone except the philosophical "everything must be a prefix". Note that unlike Mediawiki, there are hundreds of different tools in OSM, and they do not share anything except key-value pairs. So it would not be possible to make the same "smart" interface for each of them. People will have to use Q123 as a string.
Lastly, up until this morning, the Query Service hardcoded wd:, wdt:, and other prefixes to always mean "current wiki" (conceptUri), which obviously was very confusing -- wd:Q123 had different meaning depending on where you ran it, and if you used federation query with Wikidata itself, you had to hardcode a new prefix into your query to revert the meaning of wd: back to wikidata's. Luckily, it wasn't too hard of a fix that I hope will be merged soon [2].