Recently my computer main board failed and i had to switch to my old dusty 1.3 Ghz Celeron from year 2003. This rig is enough to run games like thief 2 or panzer elite from GoG smoothly, yet i found to my surprise that their frame rate suck. So i did seek out my bro old original Thief 2 CD's, installed it and, wholaaa, it runes perfectly smoothly on 1024x768. Same with Panzer Elite.

Why are GOG games slower than old originals?

I can't speak for Panzer Elite but Thief 2 might be chugging because it uses the New Dark patch which makes the game run in DirectX9. Not sure of the specs of your 2003 machine but if the card can't handle DirectX9 standards, that is probably why. I know there is something you can do in one of the configuration files to make it use the old renderer but I can't say how to at the top of my head.

Not sure if those games use DosBox, but it would be the cause if they do.

I'm pretty sure only System Shock 2 uses NewDark, last time I checked GOG's Thief 1-2 used vanilla official versions, unless GOG has made new versions of the installers I'm not aware of. GOG would probably need special permission from Squeenix to use NewDark on the Thief games.

And NewDark actually IMPROVES performance, massively, on the Dark engine games, so it wouldn't be that. As for DOSBox games, well emulating games has always been very intensive on the CPU (goes for pretty much all emulation).