FCEUGX uses hardware bilinear and deflicker in filtered mode, in unfiltered it's point and no deflicker, in original mode 240p is used so no filtering other than what is done by the hardware for the 512 to 640 scale.
hq2x is available in the recent RetroArch builds along other cpu filters and should work well with a bunch of games.
Bicubic was never used in homebrew emulators or official ones, most likely because it's a waste of cpu when you can use hardware filtering with no performance dips. Might as well mention this; the Game Boy Player used it, though it might not be the best example since the GameCube didn't do much here other than scale the image and apply motion blurring effects.
The 3DS uses it for DS and DSiware but not Virtual Console titles, the only reason I can imagine is to not use so much power.
In short it is possible but hasn't been done yet.