I've always preferred the 1990 CD's despite the noise reduction because the EQ is less harsh and the volume isn't maximized (less compression than on the 2001's). But I hear if you listen to them with a processor that's HDCD capable, the 2001's sound better.
It turns out that, like many HDCDs, the 2001 Capitol twofers don't use the peak extension feature so there is absolutely no difference in the dynamic range when they are played back with HDCD decoding. The 1997 Pet Sounds box
does use HDCD peak extension and has a significantly wider dynamic range when properly decoded (at least when I look at the spectrum in Audacity - I must admit I struggle to
hear the difference with computer speakers).
HDCD was a strange beast. If the peak extension feature is used, the playback will be inferior if the disc is not decoded with HDCD. On the other hand, a normal CD has sufficient dynamic range that the disc would have sounded just as good on a normal CD player if had been mastered without compression in 16 bits. It may be worth noting that HDCD can now be decoded in software (e..g with Windows Media Player or libhdcd on Linux).