Is creating a non-existent link the only way to underline something???

Does using two underscores translate well to a bold word, or should that make an 
%%(text-decoration:underline)underlined/% word??

How can I customize this and make the behavior more sane/intuitive??

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You can modify the JSPWikiMarkupTranslator as you please.  Underlining in general is something which was dropped out of JSPWiki simply because it's not used very much on the web.

However, you %%(text-decoration:underline)can underline stuff as you please using CSS/%.  This line looks like:

{{{
However, you %%(text-decoration:underline)can underline stuff as you please using CSS/%.
}}}

Or, just create a custom named style in your own CSS file and invoke it with

{{{
%%underline text here /%
}}}