I'm not sure how you've measured how often hot code reloading is used? I use it for almost all of my production pushes.

However, I agree that it's generally hard to use it for third party software; upgrades would either become cumbersome because you have to follow the same piecewise upgrade process the developer followed, or the developer would have to do a lot of extra work to ensure upgrades between releases were solid; the recent addition of atomic loading of multiple modules would probably help.