From Etymonline.com:

 Quote:
wondrous c.1500, from M.E. wonders (adj.), c.1300, originally gen. of wonder (n.), with suffix altered by influence of marvelous, etc.

I wonder who dropped e from wonders in the formation of wondrous. No one person decreed that it be dropped, I suppose. I don't know whether there is a term for adaptation of spelling to habitual pronunciation (someone here might), but I gather that the phenomenon is as old as writing.