Well, not exactly. The Nakamichi was an option all throughout the model run of the LS400, from 90-00. The Pioneer stereo was always standard, rgeradless of the year. In 01 Lexus replaced Nakamichi in their lineup with Mark Levinson because of Nakamichi's continued bitchyness (they refuse to have their stereo run through a navigation screen, hence why you could never get the Naka stereo with the nav system on the LS400, or anything else for that matter).
Basically the easiest way to tell is the tuning buttons at the bottom of the radio face. If they're slotted, so that there the part that sticks out is only the center of the dial, then its Pioneer. If its Nak, the entire dial will stick out, these are the BASS, TREBLE, MID, FADE and BALANCE dials.
Also, if there is a button anywhere on the face that says "ASL" then its pioneer. This is the Automatic Sound Leveler, it raises and lowers the volume based on ambient noise. The Nakamichi does not have this function.
The Naka is a funny option. Almost all 95-97 have it (dont know about the early ones), and many 98s do also, because in 98 it came in the wood leather wheel/HID package and most of them were shipped that way. On 99s and 00s however it is fairly rare, since both those options (the wheel and the HIDs) became standard.
Its also quite rare to find a 98-00 with the air suspension, but a lot of 95-97 have it. Go figure...
How you enjoying the LS? Sweet car huh? What color did you get?