I’ve logged a ticket against this with trac: http://core.trac.wordpress.org/ticket/20536
However, it turns out that for the time being it IS necessary, as WordPress currently (since 2.x) has a bug that DOES associate two terms with the same name to the same term_id! So it IS possible (though incorrect) for a single term to be associated with more than one taxonomy. See this bug: http://core.trac.wordpress.org/ticket/5809
It’s pretty wide-reaching so implementing the fix will need to be unit-tested very thoroughly. I’ll try to remember to update this question if there are any developments.
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