Hi Siri, I am having the exact same problem. I have been using ArcHydro for years, and am usually able to troubleshoot problems that come up, but this one has me stumped. Just last week I performed some ArcHydro basin analyses that went smoothly. The day before yesterday, the IT folks installed ArcGIS 10.4 on my machine. I then downloaded and installed ArcHydro tools for 10.4, and everything went fine up to creation of catchment polygons. Complete ArcMap crash. A catchment feature class was created, but like with your experience, the HydroID field is all "Null". I started again from scratch and had the same result.
The basins I am working on are generally small. Prior to 10.4, most ArcHydro operations were taking no more than a couple minutes. If you've found some solution to this I'd appreciate hearing about it.