MrGOTIME: They really are superior in almost every way (except for graphics, but even still). I'm not sure why, but I also found some of the tough X-Wing missions a bit more "do-able" in the 94 version.
Strijkbout: I have somewhat the same experience comparing the 1994 DOS CDROM and the 1998 Windows version as I find the Windows version harder. I think it has something to do with it using the X-Wing vs TIE Fighter engine and something in the lasers has changed either being it damage spread, laser speed, rate of fire or a combination of those, as well as that the hitboxes of the enemies may have been tighter than in the DOS versions.
That makes sense. I seem to recall hearing something about how the 1998 version treats capital ships differently or something. Either way, I've had a better go of things in the 1994 Collector's CD. Still can be pretty tough, but I imagine life is hard for a rebel pilot.