A dual link DVI can be turn into HDMI via adapter, it carries all the same data so you wont loose anything in the conversion. Its much easier to find a GPU with two DVI outs(most do), than one with multiple HDMI outputs.
The only thing a DVI to HDMI won't transmit is sound. For ease of connection with home theater, you could probably find cheap entry-level card with both DVI (for monitor) and HDMI (for home theater) like this SAPPHIRE HD 4650.