You're absolutely right of course, any way at all that you can restrict the light from reaching your sensor will necessarily require a slower shutter speed to obtain a given exposure. So cracking-down on your aperture all the way & slapping-on a 2x TC will certainly give you a longer exposure time, but the resulting hit to your image quality will likely be pretty high... To minimize diffraction (& maximize sharpness) I try not to crank down my apertures any smaller than f/16. And I'll only use a TC if the "field of view" demands it.
If you just have to have that extra 3-stops of exposure time (from f/16 to f/64), I'll again urge you to consider stacking an additional filter on top of your Big Stopper. To achive that additional 3-stops I'd use my Lee 3-stop 4x4" glass filter http://www.bhphotovideo.com/c/product/491473-REG/LEE_Filters_9NDG_4x4_Neutral_Density_ND.html; which is a bit expensive, but the resin filters are almost as good and much more reasonably priced.
Of course, if I forgot my extra ND filters (or I'm just too lazy to walk back to the truck) I'll do what ever I have to do to get the long exposure time that I want -- I'll use a polarizer even if I don't really need it, I'll crank-down the aperture to a ridiculously small size, what ever it takes...
Yeah, diffraction worries me too, but I will get to see how bad it actually is for different scenes. I am getting a .6 ND as well as part of the startup kit, so I´ll get an additional two stops there. I agree that stacking is probably the way to go, and that is probably where I will end up finally. Nevertheless, I will experiment with all kind of stuff (using the EC for instance) and see how my pictures are punished. I have also surmised that there is a limit to how many filters it is wise to stack given its impact on IQ, so I given the need for extra stops will probably have to cough up for some expensive high stop filters (hence the alluring Z system;)
With very good filters I'd probably only stack two or three max. Also I'd try and keep the aperture at around f/8 - 16 maybe f/22 if really required. It also helps to shoot on cloudy or slightly dullish days rather than bright sun. Shoot late afternoon and blue hour to get some color in your shots.
I'm getting into long exposures myself. Just recently bought a ND400 just to experiment a bit. If I like it I might buy into the more expensive stuff.