There are a few things like this in the Language I have also noticed, can't think of them off the top of my head but have a A4 page I have of EH!? WHATS WITH THAT!?
The wa/ha situation is because that wa is actually a particle of a sentence not a letter in a word...
QUOTE:
Konnichiwa
There is a rule for writing hiragana "wa" and "ha." When "wa" is used as a particle, it is written in hiragana as "ha." "Konnichiwa" is now a fixed greeting. However, in the old days it was a part of sentence such as "Today is ~ (Konnichi wa ~)" and "wa" functioned as a particle. That's why it is still written in hiragana as "ha."
Hope that explains it some what.
