at around 0.7A resolution, you start to be able to see electron density between atoms. Nobody using these methods cares about intranuclear structure, just the electronic structure around the nucleus.
Indeed. For comparison: atoms are about four orders of magnitude larger than atomic nuclei. The size of the former is generally a few tens to low hundreds of picometers (1 pm = 1e-12 m) while the size of the latter is just a few femtometers (1 fm = 1e-15 m).
People have used electron diffraction using cryo-em scopes to do sub-angstrom resolution. For example, my colleague Jose Rodridguez published this a few years ago.
The electron wavefunction scatters primarily off the nucleus potential. The electron cloud acts to screen the potential, but this effect is weak and not easily detected in the scattered wave.
