I use a combo thermo/sight glass in my HLT, thermo only in my MLT, and sightglass only in my BK. The sightglasses are both as low as possible to maximize usability, and I've had no issues with the thermo in the combo one being so low. The thermo in my MLT is a little less than 1/3 of the way up, so that it is somewhat centered in the mash but still low enough to be useful for 5 gal batches. I also have a thermo in the output of the HEX so that I can compare incoming temps with the center of the mash. It works well for me and my system/process (ghetto HERMS), but everyones is different. IMO it's really about personal preference and how you will be using your system.
I use the HEX as a chiller also, and using the thermo in the HEX enabled me to avoid the need for a thermo in my BK.