If you are in a hole now, my first advice is to stop digging!
By that I mean as soon as you do a cross up relationship or even a simple report link field without a relationship between two applications, they become essentially one giant application under the covers. So from a performance point of you you will contaminate the new application with the performance problems of the existing application and dig the hole deeper in terms of performance for the old application.
Connected Sync tables however allow apps to share information even if say the customer list is up to one hour behind, and not in anyway affect performance. Typically those type of master files like employee list and customer lists are really good enough to be refreshed every hour. in my own anecdotal testing, it also seems to me that Quickbase has tuned the Sync process to take a second priority to regular users on the apps. In other words even if the Connected tables Sync each hour there is no perceptible performance hit on either of the two apps that are getting Synced.
As for automations, it depends what you�re trying to do, but in a simple situation where you want one source of truth for say an employee table or a customer table, it is better to have users do their updates in the original app as they will be infrequent updates. And then let the Sync take care of it from there.
However if you do find that you need automations, I do not believe that they cause the two apps to become joined from a performance perspective.
