It is not a limitation in Sonar.
I used to routinely have 4 midi keyboard controllers and a midi foot controller at the same time - with no problems at all.
Also, as far as setting midi channels and such:
1. For a synth instance that has a single instrument, just assign the Input to the appropriate midi controller you want to use for that synth instance. You do not need to set the midi channel for that one to one association between a controller and a synth instance.
2. For a synth instance that has multiple instruments loaded, you will most likely have each loaded instrument for that synth instance set to a different midi channel, to allow each instrument to process its own midi data. For this situation, you will also almost certainly have a separate midi track for each of the loaded instruments, as well. Set the Input for each midi track to the desired midi controller, and also set the Midi Output Channel for that midi track to the corresponding midi channel for that track's associated loaded instrument for the synth instance. The Midi Output Channel is a drop down located just below the midi track's F/X bin.
The only time I would hook up the multiple controllers to Sonar was when I was capturing my complete live keyboard rig. For Any traditional recording of keyboard parts, I would use a single midi controller, usually a 61-note controller - for its size. I would swap that out rarely for an 88-note controller when I was doing piano parts that were either more classical in nature, or prog tunes with crazy extended ranges for piano parts. Otherwise, the single 61-note controller works FINE for almost all that I do, as I normally record a single midi track at a time, whether that is strings, bass, each horn from a horn section, a piano, etc.
I hope any of the above helps you.
Bob Bone