First, yes, 1055 hubs have standard cup-and-cone bearings and are easily rebuildable. They are also fine hubs and, if not damaged from abuse or neglect, are well worth building around.
Second, Matrix Iso CII rims were one of Trek's house brand rims and were OEM on many of their bikes in the late 80's and early 90's. My 1992 Trek 1420 came with them and they were both durable and held true very well. The lack of a machined braking surface isn't a detriment as their braking performance is fine with decent brakes and pads. My rear wheel lasted 18,000 miles of all-weather use before the brake track cracked from abrasion.
So, your bad experience with them tells me yours weren't built with adequate and proper tension. Before you have them replaced, try having a good wheel builder set the spokes with adequate tension. I bet that will make them very satisfactory.