Farrell...
I'd like to think NO professional (or even private) pilot would ever interpret that clearence as "descend BY 5000ft". THAT is not a standard clearence.
Far more dangerous is if ATC ever start issuing clearances that ask you to "Descend (by) 5000ft".
Clearances are always to an altitude, and pilots respond accordingly. A request to "Descend 5000ft" should always be interpreted as Descend (to) 5000ft by a pilot... THAT is the standard part of the phraseology!
Although there should be the "to" in there, even if there isn't, as long as the ONLY requests pilots ever get is to descend is to something, not by something, then the system works.