When I was studying Japanese I don’t remember ever questioning this, there was so much to learn I just accepted it and moved on. Since then, however, I have often wondered:
Why is the particle that is pronounced “wa” written with the kana that is otherwise pronounced as “ha”? It’s not as if there isn’t a different kana that is pronounced “wa” all the time. Why not use that one instead?
This is probably not answerable, but just in case there is someone out there who has studied Japanese linguistics I thought maybe I could find out and put my tiny mind to rest on this one point.
When I was living in Japan, I studied Japanese there. As I remember, when I asked about this matter to my teacher, he told me that basically it comes down to changes in pronunciation over the past X-hundred years.
Before the end of WWII, as a matter of fact, there were a few kanas that were archaic (“ゑ”=“we” and “ゐ”=“wi” among others) and were kept nonetheless, even though their original sounds had changed (those two letters, for instance, were pronounced “e” and “i” respectively).
Anyway, one of those archaic things was the fact that the topic marker particle (“は”), which apparently in old Japanese was indeed pronounced “ha”, had been shifting towards “wa” with time.
In 1946 there was a big spelling reform that got rid of many archaic spellings (among those, the archaic kana for “we” and “wi”), but nonetheless retained three: “は” pronounced as “wa” (instead of “ha”) for the topic marker particle, “へ” pronounced as “e” (instead of “he”) for the particle that indicates direction towards something, and “を” pronounced as “o” (instead of “wo”) for the particle that indicates the direct object (although it has to be said that in certain circumstances “を” can end up being pronounced as “wo”; usually when it comes right after a syllabic “n”).
It seems that whoever was deciding on what to get rid of thought that those particles were too important and too widely used to go around changing them willy-nilly. Or something like that, i guess.
In any case, summing up: It seems that this is the result of run-of-the-mill divergence between the spoken and the written language. The spoken language changes, and the spelling stays fossilised.
Having learned English by myself, don’t I know about that…