They're referring to case length (or length of the body excluding the inlets/outlets). Example: When someone says 22" Magnaflow they're referring to a muffler with a body of 5Hx11Wx22L. In this example the case length is 22" while the overall length (which includes inlets/outlets) is something like 28".
Also, when it comes to pipe ID vs OD, ID is the inside diameter and OD is the outside diameter. Example: a 3" ID muffler will slide over a 3" pipe while a 3" OD will only butt up to 3" pipe.