In Config Manager --> Misc. Tools --> Script Reference
You can check if call type or skill group is directly referenced by a script or not. Its gonna show you the refernce in active script as well as ther prevous versions of script.
No there might be indirect references, which you may not be able to find out without manual configuration audit and those references are like dynamically setting call type, the skill group referenced under enterprise skill group etc.
But as far as i know there is no database query which will tell you about this references.