Yes. 1.0 was written in the MS-DOS era, truncates quality to 15-bits, has buggy alpha and uses basic Median Cut algorithm from early 80s.
2.0 is by now a totally different program, with expanded and improved algorithms (with bits of machine learning) and uses 128 bits per pixel precision (SIMD+multicore optimized).
pngquant2 should clearly beat pngnq.