Thanks for your interest in bonzai3d. We have been hard at work on bonzai3d version 3.0 -- and formZ 7.0 at the same time (which utilizes an updated / extended version of the bonzai3d interface). If you would like to sign up for the formZ 7.0 Beta version, you can do so here:http://www.formz.com/products/formz/formz7beta.html
Large numbers of objects in a file can eventually cause formZ or bonzai3d to slow down, but if you convert them to a Reference Object (with the tool on the Group tool row) then you should be able to generate a file that performs very quickly with large data sets. We are also working on enhancing large data sets right now, so the next few updates should show some dramatic improvements in this area.
We should probably note that formZ and bonzai3d are probably best though of as "hybrid" modelers -- that offer Solid Modeling, Surface Modeling, and NURBS Modeling -- all side by side in the same project -- so you can choose which methods work best for you at any given time.
Also, we have been expanding the Webinars for formZ and bonzai3d (and we will continue to do so). If you like, you can see replays of past webinars here:http://www.formz.com/webinars/webinarReplay.html
Give it a try, and let us know what you think! (And if you post on our forum we can give you a reply much more quickly...