The Natami is likely to suffer the same problem that plagues most niche system, while it will run legacy software, the number of new packages developed specifically for it may be limited.
That may be true, but if they produce proper drivers it'll still benefit from the improved graphics modes for the base system for RTG friendly apps, and the performance will still benefit most old M68k apps, and if they get decent compiler support for their new instructions for N68050/68070 they might get even more substantial performance boosts.
There's clearly still quite a few classic users that refuse to consider an x86 or PPC system that would still like those performance boosts, and for whom the boost they might get from a Natami might be enough to let them stay with a M68k compatible system for much longer.
It seems the Replay will be perfect for a low end classic replacement for a lot of people, while Natami will push the performance boundary - I think there's plenty of room for both. Neither need huge sales numbers to be viable and both will benefit as FPGA prices go down and size and performance keeps going up.