Don't forget that your shrimp will decrease breeding in winter, which you are approaching!
I would maybe change 20% water for a month and see if that makes a difference as you may still have a quantity of tap water in the tank if you are doing small changes of 10%. Not a lot of point though if you plan to reset the tank with new substrate!
As you were using tap water at the start and that had a higher PH then the soil would have exhausted quicker so it may be a good idea to change the substrate. As you are using RO now the soil will buffer much longer and it looks from the last picture of the tank that there isn't too much grown in to make changing the substrate too difficult? It wound be easier to start the soil in a bucket for a month and then run the new setup for a month, this way the shrimps only need a new home for a month and maybe the CRS could go in with the bloody mary (the red cherry though???) for that time? At least if you do all that soon you will be done/set for the next breeding season!
Having gone through this thread in its entirety I think the fact you started with tap water of a higher PH (admittedly only slightly) is what has caused this. Remember though, in reality it is all working pretty well and those shrimps will be used to those parameters (which aren't that bad anyway) so changing/messing will probably mean much work and loss of some shrimps, however if you are up for that, all considered I would change the substrate and because you will be using RO from the start in the long term it should pay off? You may not need to change the substrate for a long time or even ever when using RO water as the buffering won't be needed if the PH of the RO water is already perfect?
Simon