DISH receivers have done a daily reboot for perhaps 10 years or more now. That it takes an hour is unusual. If you're receiver was recently installed, it may take longer than normal as the receiver gets everything set up. This is similar to the DIRECTV DVRs taking a few days to get all of their guide data straight and features (OOH streaming, OTA tuner support, etc.) enabled.
If you're typically watching TV at 3am, you may be able to change the maintenance time (depending on the receiver) to a time better suited to your household's schedule.