I have a customer that has a 48-port MS switch and is looking to connect it to their MX appliance. What is the preferred way to connect the MX to the MS, would it be via the SPF port or the RJ45 port? Is there a best practice of choosing one over the other or just a preference?
I would use a copper-based connection via an RJ45 port as a first choice because it is the cheapest solution. Only if other factors were present (such as distance, immunity to noise, etc) would I choose to use fibre instead.
There is no best prcatice for this - more personal preference and best fit for scenario.
As @PhilipDAth said, copper RJ45 connection is always cheaper. You don't have to pay for SFP's and assuming you don't need a higher end MX, you can purchase to lower spec'd ones - SFP LAN ports are only available from the MX85 model and upwards.