I keep reading in the manual that the Ammo Energy Bar is supposed to be important, but all i see is that it pretty much stays full all the time, unless i do some manual shooting with the LR Rifle maybe.

Is this how it was in the original game running on original hardware ?
Or is it maybe FPS / Cycles related, causing the energy to recharge too quickly ?

I tried limiting FPS via DosBox but for some reason that causes the game to freeze on map load :/

The energy always was starting to be important on the levels with Plasma Lance. Unless you try to use weapons before researching, then it's an issue earlier.