The block chain would be larger than a less used crypto, yes. The expectation is that when the level of scale is acheived that this becomes a major concern, time will have been spent on technical considerations to adapt the protocol to minimize the effect. Companion technologies like the one being developed by the Open Transactions team, or a “mini-block chain” may be two of the ways that this could be done.
The Nu development team is very interested in the OT project. Microtransactions of NBT are something that I believe are going to be essential for the long-term success of NuBits, so if OT is the answer to making it useful, I think it’s well-worth continuing to research the integration of the project as it matures.