So, i decide install some mods, and as far as i know all mods requires 1004 version or something like that. And here's a question: how can i change version of the game in GOG galaxy client itself?

This is not true. There might be some old obscure mods that reqiure downgrading, but most, and I think all major mods, work with a fully updated game.

Well, the thing is, i want to play STALKER Complete 2009, mod requires version 1.0005, but you say mods working on a full updated games. So, where is the truth?

I never liked Complete mod, I never played it, so I can't be certain, but I suppose it will be working with the latest version (1.0006) which is virtually identical to 1.0005 (AFAIR, the 1.0006 patch was less than 20MB). Mods for 1.0005 usually work without problems with 1.0006. Just backup your game folder and try it.

Yea, I think the 1.0006 patch just patches multiplayer.
Though I'd still recommend the Starter Pack 2017 over Complete 2009.
http://www.moddb.com/mods/starter-pack/downloads/starter-pack-repack

Please, just DON'T play this mod.
I'm not joking, Complete is terrible, it changed too much of the game. If you wish to learn more: https://pastebin.com/6AtetpMM.

For a first playthough, I would recommend you to get the Zone Reclamation Project (ZRP): http://www.metacognix.com/files/stlkrsoc/index.html
Get the ZRP 1.07 R5 RC. It fixes a lot of bugs, and doesn't change the vanilla experience.

If you wish to add some new textures to your game, get the Starter Pack 2017 that FLX83 said above.

Good hunting, stalker!

I just want to play SoC vanilla, but with better graphics, like AtmosFear mod for CoP. Can you recomend me something like that? Is this a graphic mod? would be nice. And yeah, why is everyone so dislikes Complete 2009?

The starter pack includes mostly graphical updates and the ZRP community patch. ZRP fixes many bugs which make Vanilla SOC very rough to play. ZRP does not change gameplay from Vanilla very much (you can configure what changes you want to actually use). I'd very much recommend using ZRP for bug fixes

Like rmgb said, Complete basically makes the game easier and the versions of the graphical enhancements and bugfixes it uses are all really old.

The Starter Pack is comparable to Complete in the sense that you just have to install a single pack and are good to go.
Just try it out, if you don't like it, you can just delete it from your /gamedata folder. It's not complicated to remove.

Starter Pack includes:

Zone Reclamation Project - huge community effort of fixing bugs and adding some features which we're left out of the vanilla SoC, comes with a configurator.

Old Weapons Renewal 3 for SoC - better looking sounding gun models

Photo Realistic Zone - texture pack for ground, trees, structures etc

Stalker Weather Overhaul - better looking weather and skyboxes

STALKER Shaders MAX 1.06 - better looking shaders, adds depth of field, slight motion blur (newest version uses Autumn Aurora Shaders)

FOV Switcher v17 - Field of View switcher for stalker series, comes with instructions, works for other versions of the game