All else being equal the isn't a huge amount of difference as long as in case B the open end of the vertical tube is capped (ie has a plate welded on the end rather than just a plastic bung).
In practice the best method will really depend on the fit you can achieve. Often it is easier to achieve a consistent fit with square cut ends as it is both easier to cut the ends in the first place and easier to adjust the fit as necessary. Bearing in mind also that SHS is not always quite as straight as we might ideally like.
There is also the fact that SHS, especially thicker walled stuff often has quite rounded edges which can make cutting mitres to accurate length quite difficult although this does of course depend on exactly what process you have available.
So the short answer is that you'll get the biggest advantage from whatever will give you the best and most consistent fit to start with. Which depends on the processes you intend to use for cutting, finishing and welding the tubes.
There may also be production consideration as to what is the most convenient way to assemble and weld the various parts and in what order. Typically with these sorts of box section frames there is quite a lot of effort involved in getting everything held together and in getting at all of the welds which often involves turning the assembly several times or welding in awkward positions.
Equally weld order matters in terms of minimising distortion which can be hard to control in this sort of space-frame construction without a very substantial jig. It is hard to eliminate this entirely but you can at least mitigate its effects.
Overall I would say that for thin walled small section tube (say 25x25mm x 2mm) I would probably tend to go for mitred joints, favouring capped ends more as the section and wall thickness increases.
Equally if the actual manufacturing is going to be sub-contracted it may be worth discussing with them what they think the best approach would be.