this question is about flatpak in general, not just flathub.
if a connection gets interrupted in the middle of downloading, installing or updating a flatpak, will that create any issues at all (aside from needing to restart the process)? Does flatpak make sure that all files are fully undamaged before installing them, in cases like this?
Flatpak uses OSTree to store the files related to applications and runtimes. Said OSTree is using checksums to reference files, for example to reduce space and download sizes.
AFAIK these checksums are used when downloading to verify the integrity of the download.