They are still there on the bottom version. They have black sleeves near the termination.
The top one looks like a prototype or possibly bolt down version. The bottom one looks like the actual production version. Maybe one of the Naim employee members can confirm.
The top one is is a Chrome Bumper version, possibly an early 110 converted to a 140. The bottom is an Olive version. My particular CB 140 uses the Sankens which were replaced by the Naim labelled transistors in the later models. @Richard.Dane should be able to provide more info.
So in terms of quality, is it the same between Naim NAP 140 which uses non Sanken transistors with the Naim logo vs those using Sanken?
More recent era using Sanken?
No, the first NAP140s from 1986 used Sanken 2SC2922s. Then in 1990 the NAP140 was upgraded with Naim’s own NA001s.
The NAP110 started out with BDY56s, changed to Naim NA002s in 1982. Any NAP110s upgraded with the NAP140 power supply keep their original amp boards and output devices.
between Sanken SC2922S vs Naim 001s Transistors, is there any difference in sound quality? is there a difference in the character of the voice?
is there any influence from the bass depth between the two?
The extra green earth wires were added when the design changed to NA001 devices, they help to keep the noise floor within acceptable levels.
The rubber sleeves in the top picture in the OP hide decoupling caps that you can see are fitted to the component side of the newer up-issued PCB revisions.