Im no expert on this, but Ill take a stab at it. As far as I know, ejecting a shell or in this case shells, over and over may blemish the rounds a bit, but thats about the extent of it. Regardless, if you are in the habit of racking the forend (repeatedly) to eject live rounds, just take the time to inspect these rounds and make note of any obvious damage. If there is none, other than cosmetic scratches for instance, Id say it should be ok. Also, if you havent considered this already, just dont let the shells go flying out haphazardly. Rather, keep the ejection port tilted down, and in close proximity of, something soft such as a bed, carpeted floor, etc. I dont know about you, but the idea of live rounds flying out and potentially landing on a hard surface makes me a bit squeamish.
Now, even though your un-loading method is certainly the easiest (I have used it many times myself), you might consider another way which could minimize wear and tear on the ammo and would probably be a bit safer.
This other way,
as mentioned in the Owners Manual, would be to unlock the action, slowly pull the forend back until the chambered round is fully visible and then remove it by hand. Then, with the ejection port facing down, pull the forend all the way back into full battery and allow the "released" shell to fall through the ejection port. After that, turn the shotgun over (trigger side facing up), insert your thumb into the bottom of the receiver, depress the cartridge stop (opposite side from ejection port) to release the remaining shells, one at a time, still located within the magazine tube. Finally, inspect the chamber/weapon to insure all rounds have been removed.
So, unless you are in a massive hurry, this method might be the best choice if you are needing to regularly load/unload the same rounds or any rounds for that matter. Also, as mentioned before, its just a bit safer.