Currently, if you run Black Mesa’s hammer.exe, Steam thinks you are running Black Mesa. Other than racking up many hours “playing” Black Mesa, this also makes it so you can’t launch Black Mesa from Steam. A workaround is to launch bms.exe itself (thanks, Daz 
).
It would be nice if running Hammer didn’t count as running Black Mesa so it would be easier to manage and one less obstacle for newbie mappers. 
That is what I noticed as well because I could not run any other games or exit Steam without terminating the process.
I’d like to bump this thread to state that this issue is still happening two years later. I don’t know if this problem is due to the code of the BM build of Hammer or an issue with the Steamworks API integration, but it’s really annoying to crack open Hammer for a few minutes, close it, and then come back to your computer later to realize that Steam has been counting you as ingame this whole time and you have to kill the process to play anything (including Black Mesa!)
Yes, i’ve noticed that. I almost posted this bug in the forums. It’s a bit annoying for me because i always want to know how many hours i’ve played.
Founded in 2004, Leakfree.org became one of the first online communities dedicated to Valve’s Source engine development. It is more famously known for the formation of Black Mesa: Source under the 'Leakfree Modification Team' handle in September 2004.