i was wondering the same thing. having barely just installed DTR, it's throwing some really odd urls using sh404sef... i wondering if that's what's causing a "Flooding" error message i keep getting during test registrations
I don't think there's a specific plugin yet, but I use sh404 with DT Register just fine on my site. I had an issue a couple months ago, but it was fixed through a ticket and I believe added to the recent update.
I have my sh404 config using DT Register with default settings... but you might try setting it for "dtregister" to use default Joomla SEF routing. I've done that on other sites before with DT Reg.