Just make sure you *do* plug them, the burnthrough on a D12-0 (for example) is quite capable of separating your rocket at the most inconvenient time, and probably isn't too good for it either!
I found out the hard way about this :-( I would recommend plugging well in advance with epoxy, and making sure its properly cured. Not mixing up some5-minute on launch day and getting it wrong :-(
I've also seen hot-melt glue used with equal success, and if you decide you want to turn your D12-P back to a D12-0 you can easily peel out the glue.
Alternatively I guess you could use a blanking disc in front of the motor, though you might end up kicking the casing, which may or may not be a bad thing.
Oh yeah, I'm referring to Estes motors above. No personal experience of AT, but as others say the ejection charge is easily removable.