I've got Eador MotBW from humble bundle and it is fine game, however I am experiencing overheating issues with my pc when playing. Fan is blowing full speed after two minutes into game. All the details are already set to low and it still overheats. The game itself runs fine and smooth even on higher details.

Yes, I have notebook. Yes, it is old. But it can run War Thunder fine without overheating. Is there any fix/solution/workaround for this? Or just screw it and buy Genesis instead?

V-sync?

Tried with and without, no effect.

How many FPS with and without?

With vsync its mostly 30, sometimes 40.
Without vsync its something above 40, more or less stable.

Hmm, that's not much, reducing FPS is probably not the solution you're looking for. :I
Well, you can at least try demo of Genesis (only in Russian though, but this shouldn't be a problem for testing) - http://www.gog.com/forum/eador_series/where_is_the_demo_of_this_game

Game became playable year later after delayed for year release. Programmers lacked "something" to make game optimized. Either time or skill. Or both.
If your notebook doesn't support at least 1024*768 screen, you wouldn't be able to play Genesis.
Otherwise, go for Genesis - it would run much faster because it doesn't use animation.
Especially if you tweak ini file:
Open with notepad or any other similar program Eador.cfg.
Decrease Sleep time and Refresh delay, set Lake ships to 1.

Have you already checked if running it in Compatibility Mode makes a difference (e.g. for Windows XP or even older)? Right-click the game's shortcut => Properties => Compatibility tab