There was a long discussion in uk.rec.aviation.soaring some time ago about red arrows infringements. It turned out that some programs (can't remember if NotamPlot was included) did not pick up on the NOTAM, but Spine did.
I'd recommend you to do a search for "red arrows" in that group to read the discussion.
Including aerodrome NOTAMs is a huge processing overhead, plus you will have a vast number of extra entries to check through each time.
I'm not convinced that making this the default is a good idea, but if you feel safer including this option then please do so.
Perhaps posting your concerns to the newsgroup will elicit some different opinions.
Thanks for raising this matter.
By the way, I think you meant Aerodrome, rather than En route in your last sentence.