Welcome David!
I think you’re on the right track here. In the Customer table there is an “Inactive” field (visible on the Kinetic screen but not visible on the Classic screen) that should begin to solve ONE problem. There is NOT such a field on the ShipTo table, but you can add a User-Defined (UD) field and make it function similarly.
Your usage of Customer Groups and Attributes looks to be right on point.
At the ShipTo level, as you say, there is no “Attributes” functionality out of the box, and if that feature is very important to you you might consider making the ShipTo into a different Customer, and then using the National Accounts functionality to relate them financially (that has other ramifications as well that might make it impossible, but it’s a shot). Alternatively you could create a User-Defined sub-table to the ShipTo table and add an “Attributes”-type functionality, but that would be some work.
It sounds like you have a lot of data, and over time it’s accuracy has, um, drifted. That is inevitable to some extent, but the best way to counteract it is to have solid processes (written down) and lots of training. It’s boring and time-consuming, but it’s really the only way.
There will ALWAYS be tribal knowledge. That’s what makes some employees valuable… but tribal knowledge should be an ADVANTAGE and not a REQUIREMENT to get the job done in the first place. It’s a fine line that moves.
Good luck!