How safe is it to upgrade apps using Aptoid?
You're correct. When someone develops an app, said app passes through a phase of signing. The signature consists of a RSA certificate amongst its parts, so it's univocal (hence the fact that, if you unpack an app, alter it, sign it with another signature and install it, the Play Store won't show any updates for said app).

Just as the Play Store, even Aptoide, by default, shows an app as updatable only if the signature of the APK in their repository corresponds to the signature of your installed app. This behaviour can be modified by unchecking the appropriate checkbox in Aptoide's settings.

Lastly, since altering an app and repacking it with the original signature has limited probabilities of success (tried that myself, but to no avail), updating your apps via Aptoide is generally safe, providing that you leave the abovementioned checkbox selected.