I have used Circuitworks a lot. I have not experienced your problems of extreme slow CPU and I have many PCB assemblies with thousands of PTH, NPTH and components. Everyone's situation is different, so here are some general findings:
Just about every Circuitworks - Solidworks issue I have experienced is with PCB geometry, not any component geomtry.
All eCAD file translation out cannnot handle radii, circles are OK, instead outputting chordal derivative. If the eCAD translator sets a very small chordal deviation, all your radii can be thousands of elements.
Many eCAD output on holes and board corners is inconsistent: PCB corners are sub-micron radii or chamfers, holes are 2, 3, 4 items overlapped. Occasionally PCB holes of multiple circles will be different size, again by microns, creating multibody solids where there should be just one hole.
Circuitworks library function is actually as close to an epitome of CAD simplicity as it comes. Provided you let Circuitworks make its own component library of silkscreen outline based block solids. Many people lust after JEDEC standard component library, Pin 1 etc: just added complexity to something understated, simple and robust that Circuitworks got right.
Some electrical engineers will use component outlines from dubious sources, i.e. IGES files into eCAD. Then, that same IGES file retranslated... This is often thru-hole connectors. I re-download them in parasolid or STEP and put in clean models.
I group all PCB components into a folder I name "COMPONENTS" then suppress that folder.
The only Circuitworks custom setting is to automatically put a fix geometric constraint to every component and the PCB.
Lastly, I use Circuitworks full that comes with Solidworks professional. I found Circuitworks Lite to be marginal usability. Changing PCB geometry and holes and outputting BRD file for eCAD is very worthwhile practice.