Slicer should be able to handle your models without problems. SPL brain atlas in has over 300 structures and you can visualize and manipulate them easily. New markups widgets can display/edit thousands of labels (latest stable version slowed down after a few hundred labels, but markups were completely reworked in nightly versions).
You can still use VTK, either from C++ or Python, but you get development and maintenance of tons of features for free. You can explore models, dissect/assemble skeletons in virtual reality (just install VR extension by a few clicks), do morphometric computations, process models along with corresponding volumetric images, simulate soft-tissue deformation, run data analysis using Jupyter notebooks, etc. Extensions that you contribute to the Slicer app store are built automatically on Windows/Linux/Mac and made available to interested users by a few clicks. You can also create custom branded application, with your extensions bundled and all other extensions and modules that you don’t need disabled (see for example SlicerCMF, SlicerSALT and a number of commercial applications).