Will installing a thermowell cause my thermocouple to register temperature changes slower than it otherwise would?
Yes, there will be a slight delay when using a well as opposed to not using one. This is one slight disadvantage to using thermowells. You need to decide whether the advantages of using a metal or ceramic protection tube around your temperature measurement device (i.e., protecting your equipment from being damaged) is worth the price you pay in slightly slower temperature readouts.