reactorshell,
there are several issues here based on what you've said:
1. you need as accurate a temperature of the exit stream as you can get. two of the big players here are mixing and if you are dealing with a gas stream, thermal radiation from the bed and adjacent equipment.
the thermowell error for that measurement can be easily estimated. if the error is high there are thermowell design and sensor location options that can be used to reduce it. shielded /finned sensors can be used for that.
2. the temperature variations within the reactor are difficult problem. the measurement error (assuming you have calibrated and matched sensors) is a function of the thermal environment at each measurement location.
flow distribution and the temperature gradients within the in the reactor are critical. in one reactor we were seeing 50 Deg C changes in a 10 cm zone. the several sensors were only registering the slightly different placement within the reaction zone.
of course the reaction zone shifted with composition and catalyst activity, etc. and did little to contribute to measurement certainty or confidence.
without measurment errors, who could the process designers blame?
simply put, a traceable temperature measurement can only be obtained where the process temperature gradients are small. that is a tough requirement within a reactor.
3. you can measure tube skin temperatures but they have to be installed (welded in place) and they have to be the right sort for your application.
a thermowell temperature is okay, but you have to be able to define or identify what is being measured at the sensor location.
your concern about the thermowell blockage cause a change in flow distribution would have to be sorted out.
in the absence of radiation, most thermowell measurements report within a few degrees of the fluid temperature at the point of measurement. that is where the big disagreements begin: what is the sensor seeing in the reactor.
good luck,