Anyone know if mods from the Nexus website are compatible with the GOG version? I had a bit of trouble modding Witcher 3 because not as many mods for the GOG version than Steam version.

If the file structor is the same, then they will work. Many of the mods on the nexus are still for the version of the game that was not built for the japanese and taiwanese versions (refered to as Pre-Patch). Those mods should still work on the GoG version, but ones that have been updated to work Post-Patch might have problems. You will also need to learn how to merge mods instead of drag and drop or relying on NMM which can only install some of the nexus dogma mods correctly (mostly due the majority of mods being part of an archive that holds everything in it).

Mods work perfectly fine with the GOG release, as TheMrHuggles states

Quite simply what you're saying isn't correct, No such thing as Steam mods, or GOG mods
They are identical, and usually work for every game, irrespective of the store client used.
Individual game updates, specific to one site, can cause issues, but it's not because of the site, it's because of the game version used.

With W3 that was the GOG GOTY edition, which is a different version to Steam's.
A very mall difference caused by integrating the DLC in one package.
it affected the few mods using the Main Menu, and that issue was fixed by this mod.
UPatch - Unification Patch by Wasteland Ghost=2134
Mods that check for installed DLC, need the correct script merger edits, to stop the removed DLC check being reapplied.

Even SW (Steam Workshop) mods are no different than NM (NexusMods) versions, except in the folder location they go in.
SW forces mods into it's own folder system, whilst NM (and GOG), use the games normal folder structure for mods.

I've never use SW, as it forces auto game, and mod updates, which can, and often will will break your other mods.
It's never stopped me downloading (Subscribing), just long enough to get a specific mod.
Make it into an archive, with a corrected folder structure.
Then you must Immediately delete the SW mod, and unsubscribe, to stop Steam downloading it again.

Biggest issue with SW is you must own the game on Steam to download the mods.
That's all kinds of fucked up, as mods should be freely available to all owners.
No games should support SW because of this, unless they never get sold on another store client., or on GOG.

Summary (TLDR)
There is absolutely no such thing as a "Steam Mod", or a "GOG Mod".
Only mods for different versions of the game. Not the damn store client.

UhuruNUru:

You, Sir, are THE MAN! Thank you for that informative, specific, and helpful post! Seriously, I have been reading through such TRASH for the last hour+ trying to verify what you've said regarding the differences in how Mods work for The Witcher 3 GOTY GOG Edition....and the sheer amount of BULL**IT I've read is staggering. Thank you for clearing this up, and, I could not agree more with what you said regarding the Steam Workshop. One of the pillars of PC Gaming is Free Modding for PC Games, and I detest anything that actively tries to chip away at the way Mods have always been handled for PC Games. Anyways, I'd better get off the soap box before I get too invested lol, thank you again for your post!
EDIT: Oh and I know I might sound a bit too excited about all of this, but I was really getting blown away by all of the Fanboy nonsense just trying to verify Mod information (really, do so many Witcher fanboys have to slam Elder Scrolls games just to prove their love for the Witcher? We're not allowed to enjoy both without being flamed? Come on, guys, leave that for the Console-Only crowd, PC Gamers used to be above this, didn't they??). That said, I was literally cheering when I saw a post that skipped through all of that and got into the HOW and WHY promptly.Thanks again UhuruNUru.

I got my ultra high end gaming PC to mod Skyrim in 2013, and spent many months planning both the PC, and learning how to mod that game, and other Bethesda games, I became part of the Mod Organizer support Team, pretty much from the start, because of that prior research.

Skyrim was the main reason the Steam Workshop was created, and the very first Workshop game.
Bethesda Softworks, and Valve expected it to dominate within months, and would have forced paid mods much earlier if it had.

After about 18 months of that, I started to mod many other games, and still mod every game I play to some extent.
The good mod user, is highly critical of every game they mod, but don't mod games they don't like, they mod games they love.

You will all ways get the one game fan boys, but unless they are very critical of that one game, their opinion is usually worthless.

I think Elder Scrolls are mediocre as RPG's and that has got worse over time, but they are by far the greatest modding sandbox ever made, the Vanilla games never really interested me as much as the modded game, with Enderal better than Skyrim in my opinion.

Witcher 3 is still my best ever RPG game, but not as good for modding tools.
CDPR has never understood the importance of providing the Tools from the start.
Red Kit only came out two years after Witcher 2, and whilst they were awesome tools, hardly anybody was playing the game by then.
Witcher 3 tools did come out within months of release, and were primitive, but because many more players were still playing, many more W3 mods have been created than W2 ever had, but nothing like the BGS mods

Whilst BGS have taken months to provide tools, the fact the each Engines an evolution, has allowed the community to use the previous games tools to start serious modding from day one, it's that community over many games that created the phenomenon that is Skyrim.

Where CDPR beat BGS hands down, is in embracing mods that improve the game, every major patch CDPR released made half my mods obsolete, as they became part of the base game. BGS never do that with their current game.

I take my modding seriously, but switch games constantly (I have over 500 games ready to play instantly, some with as many as 10 modded versions, on 2 TB of SSD, and 14 TB of HDD (Still need more space).

Mod Manger Choice
The best general advice, is try to find the most advanced mod manager for each game.
Usually that manager is created during the height of modding activity.

I use the user name Uhuru N'Uru, or as close as I can get on every site, and always use this avatar, but never stay in one place long, as I'm constantly switching the game I'm currently modding, and often returning to a previously modded one.
When I post it's normally to help someone else, as I tend to do my own research by RTFMing to answer my own questions.