This question assumes that the X-Wing was named for the Latin letter "X". Out of universe, that's obviously true, but in-universe it isn't actually a given. An in-universe, or at least semi-in-universe, explanation would be that it is a "closest possible" translation, as is common in Tolkien's conceit for LOTR.
Disclaimer: There seems to be disagreement in various articles about whether Galactic Base Standard IS English or is being rendered as English. However, even if you think the dialogue isn't being translated, the Aurebesh is a sign that GBS is not exactly English: alternate alphabets and differing language origins at least open the door to the possibility that GBS is an independent language, being translated into English.
And if we grant this possibility, an in-universe explanation appears:
In Tolkien's conceit (as in real-world translations), the literal meaning of a word is not the only element used in its translation. "Baranduin" was rendered by Tolkien as "Brandywine," both because the meaning is similar but also because the words themselves are similar. Other words have their translations shifted to allow for rhymes, or cadence, or association/implication, or other elements of the original text which would be lost in a straight definition-based translation.
It's entirely possible that the "native" term for an X-Wing would best be translated as "cross-wing" or "star-wing" or something similar, rather than being a literal reference to either the Aurebesh letter Xesh or the Latin letter X, but was rendered in English as X-Wing because it conveyed the meaning most fully. Or, perhaps the phrase literally sounded like "ecks-wing" when pronounced, or maybe (like Xerox and Kleenex and Post-Its) the term "X-Wing" was a reference to something else entirely in that universe (similar to "Smith-Wing") and only later became a reference for all cross-shapes because of the famous fighter's design, rather than the other way around.
This answer may not work for everyone, depending on their beliefs regarding the relationship between Galactic Basic Standard and English, but it at least provides a possible in-universe answer given the constraints of the canon.