I think a lot of Japanese publishers are still trying to curry favour with the enthusiast audience on PC, those who are probably most off put by EGS exclusives. Most of them have Western offices or affiliates, and most of those offices are almost certainly feeding back that Epic is a pariah amongst the very people who will be buying their games. And while this may be a bit of bias on my part, as Japanese games are my primary interest, I think JP publishers trade on the cachet of their corporate brand more than Western publishers do.
Plus it's the whole prioritising the domestic market first situation. If EGS is unattractive to Western gamers, it's wholly unattractive to the unique quirks of Japanese gamers. Valve has put a lot of work into understanding the Japanese market, building relationships with developers and slowly establishing itself as a presence in the market. PC gaming may be small in Japan, but it's clearly an emerging presence, and all of that is down to Valve putting in the work.
So imagine a Japanese publisher telling their domestic customers that they can't use pre-paid cards to buy their games on PC because it's on EGS and Epic's minuscule cut prevents them from doing pre-paid cards sold at Yodobashi Camera or whatever.
I guess if they only saw PC as a Western-only thing, and didn't really understand the market, and Epic came to them with a giant wad of cash they'd possibly do it. But it's clear to everyone that PC is a potential growth area in Japan, so the needs of that market will always dictate where games get released. At this point doing an EGS exclusive in Japan is akin to releasing your console game exclusively on Xbox.