The main requirement here is temperature resistance. A 3D printer extruder is very, very hot, and will easily exceed the ratings of many typical silicone glues in normal service or during a runaway event. (You should always plan for an eventual thermal runaway. They're alarmingly common with cheap kit printers.) Even high-temp glues will not survive the temperatures an extruder can reach at full power if the firmware locks up.
Muffler putty is popular for fixing thermistors because it's one of the few widely-available ways of attaching a thermistor that will easily withstand the heat. In fact, it will survive after the aluminum hot block melts. (Yes, that can happen.) But muffler putty is fairly brittle, and has a different coefficient of thermal expansion from aluminum, so there is some risk of the thermistor detaching over time. I really don't recommend puttying thermistors used in extruders -- many people do, but it's less robust and less secure for long-term use than the proper hardware fixing methods found in modern hot block designs like the E3Dv6. The temperature sensing is sufficiently fast and accurate simply by putting the thermistor into a pocket in the hot block, without any kind of potting around the glass bead.
High-temp RTV glues are very suitable for heated build plates. Pretty much any RTV (such as from your local automotive repair store) is fine if you just want to attach a thermistor to a plate. However, silicone heaters will require silicone adhesives. I've had good success with Dow Corning 736.