It says in the library, "Pillars of Eternity + 3 DLC". Unfortunately I can only download 2 DLCs, because the third one is not there.

There is:
DLC: Pillars of Eternity: Kickstarter Item
DLC: Pillars of Eternity: Pre-Order Bonus Item and Pet

Maybe the bonus item and pet is considered 2 DLCs?

Same here.

Thats interesting as I only have the Preorder one like you it says 3 dlc on the front.

I did wonder where the kickstarter stuff was, probably punishment for being too quick of the draw redeeming my code or some such. I also have a lot of meaningless 1mb placeholder cruft in the bonus section stuff like product_bonus_52123.

Mine says 4 DLCs and lists three- Kickstarter Item, Kickstarter Pet and Pre-Order Item And Pet.

Hm, i'm KS backer and i'm only got pre-order item/pet, no KS item...

The last one is the documentary which hasn't been completed yet.

For DLC missing from your account, you might want to give a try to the solution proposed in this thread:
https://www.gog.com/forum/pillars_of_eternity/gogcom_downloader_has_stopped_workingcant_download_combined_bonus_content_pack

Keep in mind that the number of DLC sated in the game card title might be wrong (mine says +4 DLC, while I get 3 only ; the error is in the title, I'm getting all bonus I'm entitled to).

If you pre-ordered the game, you should get 1 DLC:
_"Pre-Order Bonus Item and Pet"

If you backed the game, you should get 3 DLC:
_"Pre-Order Bonus Item and Pet"
_"Kickstarter Item"
_"Kickstarter Pet" (only for backer at a $50+ level)

Thanks vv221 the account refresh fixed it now it says 4 dlc and I have the kickstarter dlc
As mentioned the preorder dlc may be one download but must count as 2 dlc.

Happily the refresh got rid of those placeholder bonus items. Of course I find this out only after emailing support ah well.

I backed the game during kickstarter. I also tried the refresh, but there are still only 2 DLCs. It would appear that I am truly missing the 3rd DLC "Kickstarter Pet" or it's a typo like with your titled description.

That's it! I was only a $20 backer, so Im not entitled to the extra reward. I also checked the official website to see what version I had, it states that I have the Kickstarter Hero Edition. This only gives me:

Includes the base game of Pillars of Eternity. Added bonuses include the Giant Miniature Space Piglet and Gaun's Pledge pre-order items.

Problem solved. Thank you for your help!

Ok, from KS page, 20$ reward tier:

For early backers only! DIGITAL DOWNLOADABLE COPY OF PROJECT ETERNITY. This limited price point is only available for the first backers of PROJECT ETERNITY. All Kickstarter backers will receive a special Kickstarter only in-game achievement and item. (The item will not affect the game's balance).

Of course the achievement is steam only, but what about this item? Shouldn't we get it?

EDIT:
NVM, refreshing my account did help.