How did you assess this? Looking at the raw images is not the right way to assess SNR in these types of data. There is very strong contrast in the angular domain, which also implies that most of each image will be very low signal – but crucially, those regions where the DW gradient is close to perpendicular to the fibre direction will have relatively high signal. I’d recommend looking at the estimated fODFs to get a feel for the quality.
Well, there’s nothing overtly wrong here, but I find it’s hard to tell from the tractography output. It’ll depend on all kinds of other factors, like the use of ACT, and the threshold used in tractography, and the specific algorithm used to derive the fODF (which I assume was different between the single and multi-shell analyses you’re showing?).
Well, it makes things a bit more complicated, but nothing that can’t be dealt with reasonably easily. You just need to be aware of it and make sure you deal with it appropriately. The new functionality in mrhistmatch was added to deal with precisely this issue.
Also, on a Siemens scanner, you can turn off all the adjustments that would lead to scaling differences – see this post in the thread you mentioned. This means that you can avoid these issues altogether, and concatenate the data without worrying about scaling differences. The trick here though is to make sure that only the first scan is calibrated, with all adjustments turned off for subsequent scans.