However, when I add the organizationId( or the organizationId/networks) I get a 404 error.
I tested the method with the other networks and only one network returned with 200.
I'm not sure I'm following you. The call https://api.meraki.com/api/v1/organizations/{organizationId}/networks It needs a OrgID not a NetworkID. You should be able to list all the networks from that given Org. If it still fails for the same Org , I would open a ticket.