In SEM, measured spatial positions are corrupted due to both drift and spatial distortions. But these two distorsions may be corrected by performing prior calibration. Follow:
Sutton et al., " Metrology in a scanning electron microscope: theoretical developments and experimental validation ", 2006 - https://hal.archives-ouvertes.fr/hal-01644898/document
Sutton et al., " Scanning Electron Microscopy for Quantitative Small and Large Deformation Measurements Part I: SEM Imaging at Magnifications from 200 to 10,000 ", 2007 -
Article Scanning Electron Microscopy for Quantitative Small and Larg...
Sutton et al., " Scanning Electron Microscopy for Quantitative Small and Large Deformation Measurements Part II: Experimental Validation for Magnifications from 200 to 10,000 ", 2007 -
Article Scanning Electron Microscopy for Quantitative Small and Larg...
Zhu et al., " Quantitative Stereovision in a Scanning Electron Microscope ", 2011 - https://hal.archives-ouvertes.fr/hal-01644885/document
Cizmar et al., " Real-Time Scanning Charged-Particle Microscope Image Composition with Correction of Drift ", 2010 - https://ws680.nist.gov/publication/get_pdf.cfm?pub_id=903741
What to you mean under "vertical resolution"? Stereo reconstruction of heights on an image? It is a calculation intensive procedure, one of the main errors of which is an error of tilt angle measurements, but it has nothing to do with electron optics or electron interaction. SEM stages are ill equipped for tilt angle measurements.
The SEM image is constructed by correlating the secondary electron intensity with the raster position (x,y). It is possible to extract depth information by scanning the sample at various tilt angles, but the z data will be less accurate than the x,y data.
In a relatively new approach, the data from different sectors of the BSE detector can be used to perform a similar reconstruction. I'm not sure how sucessful it is.
Hitachi recently enhanced the resolution to resolve individual atoms based on the so-called atomic-resolution holography electron microscope technology. This is part of the emergence of quantum metrology.
Check out:
[Retrospective] Chapter 04 from Inada et al., " Hitachi’s Development of Cold-Field Emission Scanning Transmission Electron Microscopes ", 2009 - http://share.its.ac.id/pluginfile.php/21080/mod_resource/content/1/%5BPeter_W._Hawkes%5D_Advances_in_Imaging_and_Electron%28Bookos.org%29.pdf
Tamochi et al., " Hitachi’s Measurement and Analysis Technologies for Future Science and Social Innovation ", 2016 - http://www.hitachi.com/rev/archive/2016/r2016_07/pdf/r2016_07_101.pdf
H.S. Shinada, " Development of Holography Electron Microscope with Atomic Resolution —Triumph over Numerous Difficulties— ", 2015 - http://www.hitachi.com/rev/pdf/2015/r2015_08_117.pdf