Why did the aliens let a 50 year old ship into the Mothership?

Of course a possible out-of-universe explanation is that this inconsistency was just ignored by the filmmakers (since Independence Day is not that famous for its realistic plot).

But one could also come up with some possible in-universe explanations for this:

1. I didn't get the impression that the ship was really different from all those others, maybe they didn't change it in 50 years. Likewise they might just not have checked some kind of electronic identification number or whatever to realize that this particular ship was lost some years ago.

2. Another possibility is, that Dan wasn't so far with the Return of the Jedi reference from his comment. Maybe they really sensed something strange going on with that ship. Which might even be the reason for the tractor beam (or why they tried to open the windows to see who's in there). So they let it in to check what was going on, or what this old ship was doing here. They just didn't anticipate the humans waging such an ingenious attack that could bring down their whole mothership (maybe out of their success-induced arrogance) and before nuking this small ship just out of fear, they wanted to know what was going on with it.

Another explaination would be that space travel would have to be at light speed or greater to make it even feasible to get anywhere in a reasonable amount of time. This is where the theory of Relativity comes into play. When traveling at light speed or above, time speeds up for non-moving objects and stays the same for those traveling at those speeds and beyond. Therefore, to the Aliens, this long lost fighter ship that comes back to them, like a Trojan Horse, may have only been gone for a short time or a fraction of the 50 years it had been left on earth for, in our observation.

Advanced civilizations (space-faring) probably wouldn't feel compelled to re-design things every 5 years, (especially if their technological progression had slowed).
The aliens in Independence Day would be even less likely to do this since their whole reason for moving from planet to planet is a lack of resources, one of those mother-ships would require a lot of raw material, so a single old fighter might not raise suspicions (or even noticed).

While this doesn't address the authentication issue, the aliens could be:

• Overworked, it was a big fleet.
• Arrogant, so haven't taken any precautions against having their tech co-opted.
• Expected, many fighters from that era might exist for the reasons above.