I was wondering a bit about such functionality myself, so I thought I would have a go. I found one way that works though it probably isn't what you are looking for.
First you need the file in html format. Probably Calibre can convert, I don't know, or just rename the .epub to .zip, extract it and find the html file that contains the text.
Then open it on the ereader (rooted) in Opera Mobile. (I have a Nook Simple Touch.)
Set up a search engine like this. Tap in the icon in the search box at top right. Go to "Manage search engines". Long tap one to edit it. Change it to
http://jisho.org/lite/words?jap=+%s
Then long tap on a word in the text, adjust the selection, hit select then search (with jisho.org set as the default engine). This will bring up the definition on jisho.org.
Probably this is not any use to you, but I tried it and it worked so I thought I might as well put it up in case it was informative to anyone out there..