Support for adding custom SSL certificates to the snapd daemon has landed in the 2.45 release. These certs will then be added to the trusted certificates pool of snapd for the store communication.
Custom certs can be added via the snapd configuration system under
E.g. add via:
# snap set system store-certs.cert1="$(cat /path/to/mycert)"
# snap unset system store-certs.cert1