Steam – What happens if I buy a game I own on Uplay, on Steam

As of March 2016, Steam now subtracts the price of owned games from bundles, so you don't have to re-buy them.

"Past Complete Packs were sometimes a bad deal for customers that already [owned] one or more of the products in the pack," Valve added. "Either it made bad economic sense for those customers to purchase the pack, or they just felt bad about doing so since it [looked] like they were paying for products they already [had]. The new Steam Bundles system addresses this.

In fact, here's a bundle viewed from my own account:

And from incognito:

Note how the base price of the bundle is about $5 cheaper when I'm logged in.

Packages

However, it's important to note that Steam makes a distinction between "bundles" and "packages".

Packages are a fixed price - if you already own something in it, you dont get a lower price or a second copy. Bundles will take out content you already own and adjust the price accordingly.

-moistly harmless, Jul 2, 2017

With packages, the prices are fixed, and you pay the full price no matter what. So it would be silly to buy the game and then buy the game + OST package. Because you'd be paying for the game twice and only getting one copy.

Before buying the game:

And after:

That base price won't budge.

_{...I just bought a game to illustrate a point.}

The fact that you don't even get a warning at checkout means Steam considers them different games. Therefore there is no way it would tell you you own it already.