>>33782082A few options here.
First, it is reasonable to assume some pokemon aren't as easy to gender as just checking their junk. It may well be the case that scientists have been unable to gather enough evidence to decide what the gender markers are in, say, a Zapdos.
Second, some legendaries may reproduce via unusual means, or else actually not reproduce biologically at all. In these cases, the traditional dividers of "Female" and "Male" as a broad descriptor of "Egg Producer" or "Fertilizer/Sperm Producer" may not even be applicable.
Third, an extension of 1, there may only literally be one of it. In this case, gender is entirely pointless, since there is nothing to compare against.
Fourth, the pokemon may be so alien in nature that biology itself fucks off when dealing with it. We're talking about shit like Palkia, which there is no reason to assume isn't abusing some 8th dimensional warp fuckery to look the way it does.
Now, the ones we do know.
Luck is a possible factor. There are multiple Zapdos, they probably reproduce, but nobody has seen it happen. It may be the case that, at some point, some researcher watched a Cressilia become pregnant and give birth/lay eggs with no partner whatsoever, and decided we had a gecko situation on our hands.
For others, like Heatran, it could just be that they are much more predictable than other legends, and thus more scientists have been able to study them. Heatran seem to pop up pretty regularly in large volcanoes.
Then, ones like Latios and Latias just appear regularly together, and have fairly obvious dimorphism, so the only hard part was going out to confirm some biases with 'em.
>>33782147It's worth noting that assigning a sex to them is not the same as identifying their sex. While people might have had a good idea about Lati@s, until someone got down to business and figured it out properly, it would just be a colloquialism to refer to them as such.