Question 2: Wouldn't it be more convenient to store lists of things in all cases, and have the "map" version just as an optional API switch for users who don't care about order (it could remain the default)? This would help to retrieve order information more easily.
Strong support! As I see it, the mappings are causing real pain since these simply do not represent that things are, in fact, stored in order. The maps generate a wrong representation which, on the one hand, may be more convenient at first glance but, on the other hand, is confusing as soon as someone digs deeper into the API because these "snaks-order" and "qualifiers-order" hack which got implemented when everybody realized that we are missing order adds to complexity big time. Personally, I would even drop the mappings completely. Yes, the maps allow pretty fast access to values (in particular to users inexperienced in dealing with APIs) but be sure that people using the API will get along fine without them and Wikibase would have a single, clean and more consistent interface. Do not fear the change. :) I shall reiterate: STRONG SUPPORT!