Is it OK to rename an application? Let's use "Coda 2.app" as an example. If to rename it to "Coda.app":


Will it affect the functionality of the app?
Is the app still be able to access the sites data saved in Keychain previously?
Is there any problem for the in-app auto update?


Thanks.
Generally, it does not affect, but there are some apps that don't properly work when you do it. 

The only way to know is trying it. In the worst case, you can revert the changes without issues.

About accessing keychain, same thing, usually you won't have problems.

I haven't tested auto-update. I usually did it with old versions of apps, to have both old and new ones.