Githyanki from 3.5e and 4e do not have nondetection or any similar power.
In the 3.5e Monster Manual, pg. 128, gives us the spellcasting feature for Githyanki:
Psionics (Sp): 3/day—daze (DC 9), mage hand. In addition,
githyanki of 3rd level or higher can use blur three times per day,
githyanki of 6th level or higher can use dimension door three times
per day, and githyanki of 9th level or higher can use telekinesis
(DC 14) three times per day and plane shift (DC 16) once per
day. Effective caster level equals the githyanki’s class levels. The
save DCs are Charisma-based.
Githyanki from 4e don't even have spellcasting; pp. 128-129 of the Monster Manual from 4e outlines the Githyanki traits, and no spellcasting is to be found.
In 5th Edition, nondetection or similar abilities are not discussed outside of some Githyanki stat blocks.
Reading through the unfortunately sparse lore of Monsters of the Multiverse (yes, I will bemoan its lack of depth at every opportunity), nondetection is not mentioned outside of the Gith stat blocks, nor is it discussed in the much more extensive lore in Mordenkainen's Tome of Foes (yes, I will praise its depth any time I juxtapose it with Multiverse).
Finally, it is worth observing that the three Githyanki stat blocks (Buccaneer, Star Seer, Xenomancer) published in Boo's Astral Menagierie don't even have nondetection, so it isn't even a universal feature of Githyanki warriors.
There's nothing lore wise to go off, so the best we can do is make the observation that you have in the question, that, as written, some Githyanki could be under the effect of nondetection at any given time. I think it is best to view this as a niche DM's tool for running campaigns involving Githyanki - your players will have to be more creative than to just use scrying or locate creature on a Githyanki person of interest.