Not all apps will be inside My Apps, only those Google apps that were available in Google Play i.e. Hangouts

Just update. Most of your stock gapps are listed in the "My apps" in play store.

Edit: Also, play store is part of gapps. Updates are roll outs by Google. So if there's update on play store, just gotta wait (or if impatient, then get the apk from androidpolice.com)

Some of those that are not able to update are those basic phone apps, and those apps normally dont or will update together with Android version update, so no worry. Just check Google Play store every night, that's what I do.