The short answer is no. Shim can't be configured right now to use more than one SciDB port.
You can start multiple copies of shim, and use command-line options to control the port. See shim -h or man shim or the shim webpage for more about this. Note that you'll want to start the 2nd shim service also running on a different http port to differentiate it from the default shim service.
Here is an example:
shim -p 8090 -s 2239
That would start a shim server running on http port 8090 (that one could use from python or R or wherever), and talking to a hypothetical SciDB server running on port 2239. Then in python use port 8090 to talk to the 2239 SciDB and the default port 8080 to talk to SciDB on its default port of 1239.
This shows why I picked the name shim! It's a network service that sits in-between SciDB and other clients, and translates things into HTTP.
Looking back at this, I think it's more complicated than it needs to be. We should probably incorporate a way to select the SCiDB network port as part of shims HTTP API. This should not be too hard.
Is this something that you would be interested in helping with? Maybe at least testing some new ideas out?