Assuming you only have the one webhook for that survey, are you sure the survey in Experience Builder is connected to the proper survey? (I.e., can you do a new submission from Experience Builder and see that record in the proper Feature Layer?)
I see no other reason for survey submissions through EB to not trigger a webhook.
EB's survey widget is a lot like the web interface, in that each time it's loaded, it downloads updates. This is (annoyingly) contrary to the Field App version that only checks for updates at specific times. After adding a webhook to a survey and prior to submitting from the Field App, you are required to manually check for and download the newly pending update. Without this aforementioned update, submissions from the Field App will not trigger a webhook. But this shouldn't be an issue for EB (you can always try reloading the web page though).