After leaving the players maze morte was just gone. Is that supposed to happen? Does he reappear later in the game? And if so, what do I do now to progress the story?

Where were you when you triggered the Players maze? Normally your partymembers are waiting just there when you return.

I was at the eastern entrance to the alley of dangerous angles. Also when I came back I had to talk to dakkon to join my party again.
Can I hack the game or do something with its files or anything like that to bring morte back? Programmers I need you!

Morte is not necessary to continue with the story, no NPC is. One party member less also means one more free slot for NPCs you might find later and more XP for everyone else now.
Your current main quest is finding Pharod, just like it was before. The player's maze is just a side area not needed for the story. Making the Lady angry again is one of the few ways to die forever.

But wont the story be lacking something?

No, the story won't be lacking something. You're writing your own story after all. If you want a canon story read a book.

But why did Morte not wait for TNO where he left? Is it a bug?

Yes, it's a bug, it happened to me once. I always leave the party before triggering Player's Maze and TNO's tomb.

There's something that's supposed to fix this, but a forum glitch is preventing my posting the link. Try Googling for 'Planescape Torment Lost Party Members Fix'.

EDIT: This should work now, so for the record: http://planescape.outshine.com/mods/readmeplost.html

I had the same problem. Morte was dead before I entered the tomb. I came out and his gray, dead portrait was gone, leaving just me and Dakkon. Would like to get him back. Is this possible?

I think this was intended by the devs. In my first playthrough, Dakkon got killed by a mage. Unfortunately, I didn't have a Divine Censer in my inventory. You have to ressurect them asap.
Have you tried to use a editor to get Morte back?

This is an old thread but just in case people are running into this situation again, you should check something before patching or reloading an old save because I found out my game wasn't bugged. I got mazed after becoming a disciple of Aoskar, and after I got out I thought I was a victim of the lost party members bug, which was a problem because I'm playing the game on a mac and patching files in Wine (even in a special GOG-approved wrapper) can be a nightmare.

After doing a little searching, I decided to pixel hunt the entrance to the burned cathedral (seeing as the cathedral was the last building I exited before getting mazed and the archway before the entrance obscures a whole lot). Both my party members were there waiting for me.