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Systems such as electron microscopes have multiple elements for multiple usage, no one will buy a single use microscope these days. As far as I know, the glass optics are used extensively in the detectors as well as the in built camera (the one where you see your sample in real size scale), the latter being where these "perfect lenses" will come handy.
The magnetic condenser lenses are more with how the actual hi-mag images are taken.
The built-in optical camera is generally just a basic camera for sample positioning and is little more than a webcam with vacuum tightness. The detectors don't use glass optics either, as they are detecting electrons rather than photons. No focusing is required at the detector end anyway as that is done via control of the beam with the condenser lenses. None of the normal EM addons (Element analysis, Electron Diffraction, Cathodoluminescence, electron spectroscopies) work in the optical range either.
Thats not to say that these lenses aren't exciting, just not so much for current electron microscope technologies i think.