Actually, the FAQ contradicts itself. Based on the answer to this question...
Q. Are there any other fees charged when trading in multi-currency?
A. No. However, please be advised that there is a 2.5% premium when a trade involves orders in different currencies. However, this is not a separate charge. It is already reflected in the price you see.
Based on that it looks like there are indeed separate order books, but that all trades are reflected on other currency book (minus a 2.5% currency commission - which quite frankly kills the competitiveness of the order). So the moral of the story is that it's best to trade on the busiest currency. If you trade in Thai Bhat, don't expect to get your orders filled.
Bank fees.
That's way too high for a bank fee transaction, especially since MtGox is not actually doing any conversion until you cash out (and many opposite transactions will net out). More likely, they are discouraging currency trading on their platform, and pocketing the fees. Doing the math on the 8K wall for example, $127 / 1.3006 (EUR daily rate) * (1 - 2.5% commission) = 95.26 EUR (exactly where the EUR wall is). This makes the wall 2.5% less competitive in any other currency, and much less likely to get hit than on the USD order book.
or bank fees. money goes out -> transfer fee, gets exchanged -> exchange fee, goes back in -> transfer fee, you buy BTC -> Gox fee. I can see it reaching 2.5%.
No, because MtGox doesn't actually make those conversions. They just have one large account per currency and only need to transfer from one currency to another if the net currency shift drives one currency account too low. I would say that, for the most part, they are almost never incurring any cost at all. That 2.5% is all profit. In any case, I would guess that it is often unlikely that any of the cross currency orders actually get filled since they are 2.5% below market (unless there's a persistent currency:BTC spread).
Technically they are not supposed to do fiat currency exchange. It might be they do not, in fact, move funds around with each operation. However, in case, say, some Gov agency forces them to do so, their expenses are covered by the 2.5% fee.
As you say, it will definitely discourage traders from opening cross currency orders, which makes gox's life easier. (don't think they would make much in cross currency fees)