The main difference I know of is the 6 pin cdi's have 2 grounds and the 5 pin has 1. Now as to them being interchangeable I'm not sure. I'm sure if you found a pinout for the both of the cdi's you might be able to figure something out. If you have been using old used cdi's I would recommend finding an aftermarket 5 pin cdi box with a pigtail and using a wiring diagram to splice them together.

Look for something like this. I had good luck wiring one like this into my 250 Big red a few years ago. And make sure you know if you have a DC or AC ignition system. They make cdi's for both
1979 ATC110
1983 ATC110
1984 ATC110
1984 ATC125M
1985 ATC110 2 of them
1985 ATC110 The wife's
1987 ATC125M
1985 ATC250ES
1984 DX225 with 250 timberwolf engine and swingarm. Wolf in DX clothing