Cstrike folder missing.

If you have the game installed, then you have the folder. It's just a matter of finding it.

Steam/steamapps/steamusername/counter-strike source/cstrike/
 
Right click on Counter-Strike: Source in steam, go to properties, go to local files, click "Verify Integrity of Local Game Cache" After it's complete, check to see if it's there.
 
Have you run the game recently. The files for you games aren't created unless you run the game; that's why if you play Garry's Mod you need to run all your games in order to use their models, and various other files. Run you game, and it would tell you if there's a problem. The default location as jaxory said is "steam\steamapps\username\counter-strike source\cstrike. That's how all the main steam games are set up if they use source. If it's a game like fallout 3, or AA3, then it's in steamapps\common because those aren't directly associated with your steam name.
 
Have you run the game recently. The files for you games aren't created unless you run the game; that's why if you play Garry's Mod you need to run all your games in order to use their models, and various other files. Run you game, and it would tell you if there's a problem. The default location as jaxory said is "steamsteamappsusernamecounter-strike sourcecstrike. That's how all the main steam games are set up if they use source. If it's a game like fallout 3, or AA3, then it's in steamappscommon because those aren't directly associated with your steam name.

I was told by a friend that if I launch a game it would come back, but it didn't.
 
I was told by a friend that if I launch a game it would come back, but it didn't.

That's really weird because it really should come back. That's how valve games work on steam. Your game files themselves aren't saved in that user folder, they are stored in the steamapps folder. The game files are compressed into .gcf files. Once you have the game downloaded, you'll have the .gcf compressed game files, and once you launch the game itself it will create a folder in your steam user folder. This is then where all your settings, and configs will be stored. Deleting that folder will only result in you losing your settings and skins.

If all else fails I would re-install like b0bfath3r said. Delete the game via the steam game window and then delete the Counter-Strike folder in: Steam/steamapps/accountname so you can start totally fresh.
 
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