Do all the enemies rise again in the blood moon?

Yes. All enemies in the game that you've defeated come back. Bosses are the likely exception (I haven't checked yet).

This is a change to the Zelda franchise as previously enemies would respawn in you switched areas. Now, the only time they respawn is the Blood Moon.

All enemies return after a blood moon except for:

• Enemies inside Divine Beasts. This includes the unnamed Divine Beast in the Final Trial as part of the EX Champions' Ballad DLC.
• Sentries. These are the enemies on Death Mountain that appear in the quest to get inside Divine Beast Vah Rudiana.
• Master Kohga.

Lynels and Mini-bosses respawn. Mini-bosses include the Hinoxes, Taluses, Moldugas, and the EX Champions' Ballad DLC mini-bosses (Igneo Talus Titan and Molduking).