I have used everything from real good milspec bolts, to black M5 Internal Hex Socket Cap machine screws from home depot, to whatever junk came with racks and water bottle cages. The only ones I really avoided was the aluminum ones that came in the frame of some bikes. The only rack bolt problems I have seen on my bikes and the bikes of friends and family is vibrating loose. Even with heavy loads on rough surfaces I have not seen any broken rack bolts.
So my take is that unless you get some really poor quality bolts they aren't going to break or cause problems if properly installed and subjected to normal usage. If they do cause problems it is most likely that it will be because they vibrated loose not because they broke.
On the other hand I really don't see any harm in using better bolts. If I had them on hand when I was installing the racks I would use them, but I wouldn't bother seeking them out or swapping out bolts that are already installed.