Yes this is true. The earlier Naim CD players were based on an old Philips transport which proved to be the most suitable for high quality CD players. Philips stopped making these transports some time ago and although Naim stockpiled a number for new players and spare parts they eventually ran out and had to design a new range of players around a new transport. It is true that the older transports offered a better signal to noise ratio than the ones used in the newer players. However the newer players have been redesigned around the new transports and contain many other significant improvements over the earlier models.
Most people think the newer players are a significantly better.
Yes - although most owners of Naim amplifiers prefer Naim CD players but there is no reason not to use a CD player from another manufacturer. There is little consensus about non-Naim CD players amongst Naim owners. The one exception is possibly the Rega Planet which is widely respected as a cheaper alternative to Naim. Other people have had success with CD players from Linn and Audio Synthesis. In the US it is more common for Naim CD players to be used with non-Naim amplifiers where there is much more diversity in the amplifier market.