So, if the monk had Empty Body already activated and was also Hasted at the time when the spell was cast, would you have both those effects be cancelled when the Polymorph went off?
Yeah. You can
haste the t-rex, but the
haste you put on the monk isn't working on the T-rex anymore. I could see a DM going the other way with concentration spells on this one reasonably - magical effects that someone
else is concentrating on could remain in effect (though you'd lose the spell if you cast it on yourself). But for me, it's just simpler to say "This statblock is you now. You can modify it from here on out, but it won't apply when you change back."
I mean, a T-Rex Monk is hilarious and all, but the fun rapidly curves when they're spending 15 minutes recalculating their action plan based on newly powerful class abilities and synergies, and that's nothing I want to worry about.
It also makes the spell an effective debuff - if the monk retains class abilities, why shouldn't the beholder be able to shoot eye-rays from its slug eyes and hover in place? Why shouldn't the banshee be able to wail as long as the chicken had a beak from which a wail could echo forth? You'd turn a potent control spell into something much less effective for disabling monsters.
Polymorph has plenty of hilarious still built into it (my favorite use is still transforming a falling character into a killer whale because a killer whale has more HP than your typical terminal velocity damage roll), and a lot of potential flexibility (no cage can hold the mage who can turn into a mouse! Though I hope someone can communicate with beasts because when my mind is mousey I'm probably less interested in escape...), so I'm not worried about this limiting the fun potential too much. Unless your fun is in gamebreaking combos, you should be fine.
However if the spell says you retain your mind, certainly I would let the PC keep her Knowledge proficiencies. Also "spiritual" abilities if any would stay, e.g. if your race is somewhat celestial and has intrinsic defenses against evil.
I think
wild shape would be a slightly different scenario, at least in part because you do retain your mental ability scores. But I believe that's part of the advantage of using that class feature over polymorph, and part of why even the combat wildshape is limited to a significantly lower CR than polymorph.