I think I see where you're coming from. Let's see if I can't clarify some things here...
"Number of Mining Beam Nodes" has never had any influence on the ships' mining strengths. The weapon was purely designed for flavour and to make those ships a bit more unique. They would always have had the same values whether they had the nodes or not.
I think the Salvage Rig is a pretty poor comparison for balancing mining strength since it's not intended to be a mining ship. The Shepherd is better, since it's more accurately a "mining ship" with the Borer Drones. However, that's a tenuous argument because mining strength is purely mod content, and since the mining strengths for vanilla content were decided on by another (admittedly prolific) modder - and there's only like two vanilla ships that have a strength - there isn't really much to base your values on besides other mods. A lot of my mining strengths start as pretty hand-wavy values and don't get much change before I'm satisfied with them, though I do use said other mods as indicators.
Regardless, that also overlooks a potentially more important argument: you can hum and hah about the face values as much as you like, but in reality mining strength is just one more value to keep in mind alongside everything else. Balancing "in a vacuum" as it is known is strongly discouraged; you should always keep the big picture in mind.
Take the Starlifter for instance: Huge, slow and seriously easy to kill. (Have you played the "Trainwreck" mission?) Plus the ship's designed primarily for mining. It has big weaknesses and big strengths - mining is one of those strengths. I think it's allowed a large base mining strength, and if a player wants to splurge on mining weapons to push it even higher, they pay the price in a lack of defensive weaponry.