I presume if you're idea is true, if any DLC will be considered cannon, it would be Broken Steel.
My point was that it probably won't be referenced in any future games, so it doesn't matter. Whether or not Mothership Zeta (or any of the DLC) is canon will likely be up to the player. It's an open ended video game series, after all.
As for this, it doesn't remove the Cannonicity of aliens, since Recon Craft Theta is in Vanilla FO3.
True, but a player can call that an easter egg just like the easter eggs from Fallout 1 and 2. I personally consider everything official canon since I'm not all that picky, so I do consider aliens and the Fallout 1/2 easter eggs (as ridiculous as some are) canon. Regardless, I don't think it's a rule that you have to consider everything in the vanilla game canon. There's some folks who don't even consider Fallout 3 in its entirety canon.
French Vanilla DLCs are questionable, except for the location of the Pitt. Operation Anchorage was technically a non-Historical event, since it is stated that the whole thing is FAR from actual history. Point Lookout could be considered mostly canon, as the place does exist and likely didn't get bombed.
The Pitt is mentioned by one of the Lyons' Pride members, so if you consider all content in the vanilla game canon then the existence of the Pitt is canon at least, if not the side quest from the DLC.
As for MZ, it could be considered cannon, but this doesn't mean aliens will ever be the center of the games. We KNOW the aliens are out there, but this entire DLC is like a side-quest, that has no real effect on the entire world, therefore, likely aliens will have no real involvement mainstream in the games weather it is cannon or not. They will NEVER make a game completely based on the aliens, unless it is a spin-off, so stop worrying.
No, I doubt they will. Mothership Zeta is more like one of those goofy side quests that you'd find in Fallout 2.