Actually the categories + reporting tags are really designed to prevent the need for deeply nested categories (of course this isn’t going to be the case 100% of the time). The problem with deeply nested categories are many. First, new staff have a hard time getting up to speed because they need to know what’s below what and so on. Second, it can greatly increase the time to classify requests. One final issue that would be specific to HelpSpot is that since assignment is tied to categories that entire system could get confusing.
All that said, I’ll definetly note this for more thought down the road.
Also in version 2 of HelpSpot you’ll be able to build your own version of nested categories as they’ll be a new multi-tierd predefined list custom field type. So you could categorize via the custom field.