I don’t have any experience with these programs since I use Content Management Systems and these scripts have this functionality built-in.
I think you should try the program since it is very easy to install and it will not hurt your site nor interfer with search engines for sure.
MySQL programs are easy too. You do not have to know anything special about SQL. You only need to create a database and user, the program handles the rest. The big difference here is the source for the data storing. CCounter stores the data on a text file and the others on a database.
The only headache you’ll have is to configure all the links you want to track. Don’t know how much you have…