The MiniDSP SHD Studio is a much more modern component, with much better quality internals than other MiniDSP products. I would say say hardware wise the Paradigm PW Link is in a similar class as the MiniDSP 2x4HD. The SHD Studio is in a different league altogether.
Dirac and ARC are generally considered to be similarly good, with many people giving a slight nod to Dirac. I believe Dirac is much more flexible, allowing you to tweak the target curve to suit your needs exactly.
minuDSP does include Bass management upto 2 subs which is very flexible, but the Bass management part has a steep learning curve.
The benefit of a sub with good speakers is not so much better/deeper bass output, but more of flexible positioning to reduce room modes. I would recommend getting a UMIK-1 mic and downloading REW (a free audio analysis software) to measure your frequency response first, before deciding if a sub is needed.
Most people/rooms benefit from multiple bass sources, so room modes cancel each other. However, In my case my speakers when measured individually are quite flat, However when I measure the combined L+R response with a mono signal, I have all kinds of peaks and nulls in the bass region. Adding a sing sub, introduced some crossover anomaly but restored a flat bass response. With a little tweaking of the crossover, my overall combined response is now fairly flat.