route=shuttle_train versus route=train + shuttle=yes (or whatever) is a minor concern here for me as long as these tags can only be found on route-relations.

I deleted OSM ways here that were tagged with route=shuttle_train with some other tags (but not railway=track) to represent the railway tracks.
The ways had been mapped between / in parallel to the railway=track ways which already existed in OSM.

This is against the mantra "one feature, one object".

I.e. what exists in reality only once, must not be mapped by two more OSM objects, period/basta!

This applies to the Eurotunnel-Shuttle as well.

In addition, there were also two route-relations. the older, propper one, with route=train (having the tracks as members) and the newer one route=shuttle_train (with the suspicious ways as members).

In addition: routes are virtual OSM objects and must not by mapped on odes and ways but using relations. This is well established for all other public transport elements. A train carrying cars and shuttle trains fit well into the schema.

What's the difference between a shuttle train and a train?
Do shuttle_trains have only two stops? No, I guess that's not always true?

BTW: the tracks on the Hindenburgdamm between Sylt and Niebüll are also used by other trains RB*, ICE*, ...
Please refrain from adding route=shuttle_train to those tracks - that would obviously be completely wrong. tracks are tracks and trains are trains, two completely different objects in OSM and reality. Don't mix them.

Back to your question: a route-relation with route=shuttle_train versus route=train + shuttle=yes:

Once routing engines learned to make use of route-relations, the code to differentiate between the two mapping flavours is tiny - so why not take the correct one?

A shuttle train is a train with special service: route=train + some additional tags.
This would also apply for route=ferry carrying cars, bicycles, trains, ... and (!)  passengers which came by foot.

BTW: would you introduce an new tagging schema (shuttle_ferry) for ferries crossing rivers (having only two stops)? No!

I'm going to start a discussion in the community and will provide the link here later.