Most people use Hepburn romanization (I like something phonemic like Yale, better, but whatever), but different people use different systems, often just depending on what they feel like writing or even know how to write. What will happen when people start to search the site? If they search "八", will they find the questions that used はち, hachi and hati? That could be a serious issue.
We use Lucene.NET behind the scenes for search, so whatever it supports we can eventually do -- it may take some time for this to happen, though.