Since water seeps in side windows during a heavy rain, I'm wondering if I should shoot some wax treatment inside doors. Or does water drain through somehow? I know there's a small drain hole in leading edge of doors that you can see when they're open.

There are drains, on my MK2, more than a couple per door.

The BIG problem at least on MK2's has been the absorbent pad glued to the door skin.
Tends to hold water and encourage rusting.

Previous owner removed said pads from mine.

If it was my car, I would remove and inspect the inside of the doors.
Remove any visible rust scale.

I treat the actual rust with Rust Mort, which chemically reacts with rust, turning it hard, black and inert.

Por15 simply encases the rust, which would probably work on top of the Rust Mort once it has hardened.

Then I would paint the insides with something hard and shiny (not just primer), to shed any water.

But, then, I want mine to last, ya know?

Dave

The inner door skin pads in my '65 S type are intact and it seems to me water would have completely deteriorated them by now after 43 years. They help to eliminate door skin vibration and resonance. I would not remove them, and in any case (if deteriorated), it mught be a good idea to replace them. The same material is laid over the transmission tunnel and inner firewall/bulkhead.
also under the rear seat and the floor.

DynaMat is about the same principle, a self sticking rubbery/tar material used to insulate against heat and resonance.

Ex

Never had a problem with vibration and/or resonance in the doors.

Several have commented on the serious issues these pads can create.
They actually hold moisture against the skin.

http://forums.jag-lovers.org/avsn.php?1127284j74
"Inner and outer rockers are major issues on MK2s, and many times you will get a rust hole in the middle of a door or, additionally in an S/420, in the middle of the rear fenders. Jaguar used sound-deadening pads in the middle of those large metal panels to cut down on drumming noises.
Unfortunately, those pads were made out of felt or jute. When the water
dripped down inside the doors, whether or not the bottom drains mentions by Clark are clear or not, the pads get wet. Wet equals rust, again from the inside out. I had a very nice Calif. black plate late S -type (all-syncro, late brakes) that did not have any lower fender rust popping through its still original paint. But, there was a hole in the middle of one of the fenders from the wet anti-drum pad. Obviously this otherwise pretty dry car had gotten water on the pad, so, it is just a matter of time before the lower fender rust will begin showing."