Hi,
Questions regarding the CAD->OpenVSP are best asked in the OpenVSP forum.
As far as fuselage geometry, one thing I'd like to be clear with the limitations of SUAVE is that it is not CFD (unless of course you connect to a CFD code). So adding segments in SUAVE usually has very limited impacts. SUAVE looks at high level parameter of the fuselage to calculate the drag and the weights. What's important are lengths, max heights/widths, fineness ratios, and most importantly wetted areas. The benefit of segmented fuselages is the ability to connect to OpenVSP and get a more accurate estimation of these parameters to feed back into SUAVE.
These limitations are not present in Wing geometries and the small details of each segment and airfoil are used.
So with that knowledge, perhaps for your toolchain all you need to extract are the top level parameters of the fuselage from CAD.
Let us know if you have any more questions,
Emilio