Well, there are several ways of working with customers and their connections. You might find this useful: How do people monetize the use of Make? - #2 by Henk-Operative
Generally, there is nothing wrong with adding customers’ connections to your Make account. As long as you can keep the overview and don’t mind that operations cannot be traced easily.
On the other hand, I’d advise you to open (or have open) new Make accounts for your customers, which you can access as an App developer. This makes everything nice and separated, you can do your thing and if in the future the customer wants to move on, it can happen with a few clicks.
If you are technical enough, you can also use Make’s API to programmatically add connections to your Make account: https://www.make.com/en/api-documentation/connections-post#connections-post
Cheers,
Henk