The current default Apache value for AllowEncodedSlashes is Off. IIUC if a %3F sequence is sent by the client a 404 response is returned unconditionally.
The NoDecode value is a “relaxed” behavior. I guess Apache at least make an attempt: if the requested file name matches literally, it is returned (e.g. this%3Ffile.gif - but ok, that’s a bit weird case).
Changing the parameter value everywhere on the fly should be safe, but as usual the safest path is defining a prop and change its default value for the next NS release: 7.10. I’d avoid a new UI checkbox because the new default behavior shouldn’t harm in 98% of cases 
That would be the same strategy to be applied here: