Multiplexing thermocouples, what to look for in multiplexers?
I use DG409 multiplexers (100 ohm max) and switch both thermocouple wires in order to multiplex up to 16 devices. Ditto the cold junction RTDs and I also have spare multiplexers to give me a "zero" reference and an actual positive voltage reference of about 75mV. Done it this way for years.

So, I believe the trick is to not worry too much about on resistance but keep an eye on relative on-resistance specifications between the internal multiplexing switches. Run the mulitplexers from both positive and negative supplies because you cannot be sure about the polarity of the thermocouple signal AND you want to have decent headroom to each supply to avoid strange on-resistance effects. I use +/- 5V.

Because you are going at fairly low speed I'd hang a 10nF on the common output of the multiplexers and also consider 10nFs on each input wire to 0V.