I recall having slowdown with the Steam version of both Death End games, and recall reading that they had optimization issues resulting in that. I'm not sure if it's an issue on how the games were ported or if it's my specs.

These are the specs for my system: Win10 64-bit, Intel i5-8250U CPU (1.8GHz up to 3.4GHz), Nvidia MX150 GPU (2GB dedicated VRAM), 8GB RAM, and an SSD.
I would like to think that they'd be enough, considering I can run Doom Eternal on low settings and Senran Kagura at max, even the Neptunia games with 60 FPS, but what do y'all think?

It is actually not the port that is responsible for the slowdowns. The game doest manage your graphics card probably. That is why you have to set it to high performance graphics card in the nvidia control panel options.
https://www.guideoui.com/death-end-request-how-to-fix-low-fps/
otherwise it is using your onboard gpu.

I get really smooth gameplay after doing this.

Sorry for not replying sooner, I didn't get a notification. I tried the NVIDIA control panel and manually setting DE/2 to use my NVIDIA GPU, but to no avail. Task manager said both games were using 100% of my GPU, which's strange to me because Megadimension VII has similar requirements (same recommended GPU though, GTX 960) but it's able to run at 60 frames and doesn't use 100% of my GPU. I really like these games and want to continue them on PC but I don't know where to go from here.

hmmm... tbh I only tried DE;R 1 so far.
I will try the 2nd game and communicate how itwent.

I got a laptop with a ryzen 7 and a RTX 2060 btw.

Will also try how much GPU the game uses and maybe try my other computer with a i7 and a 1060.

It's been years and the question I posed had been long overdue for an answer. The short answer to the title: no, the (GOG) ports do not have better optimization (they're the same).

Without the requirement of a gaming client (i.e. Steam or Galaxy) running in the background only provides a 1-to-2 (if any) frame rate increase (from my observation). There's no real performance benefit to getting from GOG compared to the version available on Steam.

Hopefully this will answer someone's question when they check out the forum for the exact same inquiry.