For what I have seen so far, the need for three different web applications generally comes from the authentication requirements more than scalability/performance requirements. Ofcourse there is a performance hit if we isolate the app pools for different web applications as they end up reserving more memory. However, you get the option of configuring different authentication mechanism for different web applications.
Intranet scenarios mostly goes with Integrated Windows authentication. Partner collabortation goes with either FBA or Claims depending on the security requirements. For public facing sites, mostly it goes with Anonymous access + Windows Auth.
Update: There are other factors that can constitute a decision for going with 3 web apps instead of 1 besides the most popular being the authentication mechanism.
Architecture best practice is slightly a subjective matter in this case. I'm sharing a few examples below that still shows why you may require to use 3 web apps instead of 1 even if "authentication" was not your primary requirement based on the comment you mentioned.
- Throttling requirements and happy hours for large requires can sometimes dictate how many web applications you may need as these options are only configurable at a web application level and not on a single site collection.
- Service Connections or "Service applications available" to different sites might need a call for different web applications. A service application cannot be designed in a way that its made available for some site collections and not available for other site collections in the same web app. I have seen this become a factor during a few multi-tenant scenarios.
- Document upload size is only configurable at a web application level and not on a site collection level.
The above three are frequently encountered situations where despite using hostnamed site collections , it demanded different web applications as well. So the architecture you followed can be the right design decision depending on different factors like the above you may or may not have included. Compliance , Security , Monitoring , Performance are the major factors that I have always seen to determine the need of different web applications in SharePoint more than the mechanism behind how the urls of site collections are resolved. I hope this explains your question.