Is there an option to play simultaneous turns even after players meet each other?

No, there isn't. You can either turn off simultaneous turns entirely, or use them until the players meet.

It's so painful to play without simultaneous turns, sometimes it even takes more than 20 minutes for each turn... We were playing a 3 player game, no CPU and it got to the point where we got angry if someone got in combat...

Not really, I love HOMM3 I had gold edition years ago but never played long multiplayer sessions, then I got into Age of Wonders until last week when I got HOMMV and decided to try it and found no simultaneous turn disappointing. I mean even Civ IV does it, I loved the game hated the waiting.

At least the game reminds us that the turn has passed even if the game is minimized since the icon starts blinking that's a plus at least.