Good question. There are a few internet posts on the SD vs onboard eMMC speeds but for me that is not the main issue. The speeds should be close enough for what we are doing.
To me the disadvantage of the SD card is the extra metal contacts that have to be kept clean in a very corrosive environment. We plan to use this on an Algalita plastic pollution expedition which will test this ROV in a sea environment for two months. There will be moisture accumulation in the electronics bay and the salt air will work on all contacts. We plan to wash it down with fresh water after each use but not sure we can do scrubbing of the electronics. Those will have to be sprayed with a water proof coating before using I suspect...and still not affect heat dissipation. I have zero experience with OpenROV in salt water so we will see. It just seems that an eMMC load would be more reliable provided it is time stable and doesn't corrupt with use.
The main advantage to the SD card (providing it is self booting without using the BB boot button) is the possibility of lot of extra memory for expanded functions. But most of the image processing that I have in mind should be capable of being performed on the cockpit laptop as post processing. There are however lots of things that can be done realtime using say OpenCV to do image processing. One thing that comes to mind is to do auto ranging by processing the angle between the two laser spots and then compute the range knowing their separation. This can be a very simple opencv program.