Well any time you do exroot or anything where the linux system will be using a second partition will affect the entire system. How much, it’s hard to say, but it will affect at least a bit. Even if the system does not use the full read speed, it’s always better to have the margin. The system needs to look up things on the external partition any time you do something on the system.
It is also great to check what chip is being used in the memory controller of the microsd / usb stick, they are not all built equal, some are really fast at looking up data and have large cache, while others might be lower quality chips where steps were skipped to keep the price down. If you stick with brand name cards / sticks, the issue is still there, but in a lesser extent.
Caching of the rules yeah, that is not really the issue.
A personally like to tinker with the partition and change things on my pc, and then just move the usb stick over when that is done. More convenient 
I prefer the usb stick in that regard as well, vs the microsd card that needs an adapter and a reader, not just plug and play in all devices.