You can hide the Searchbox that appears in the navigation bar using the following powershell

Connect-PnPOnline -Url "https://[tenant].sharepoint.com/[site]" -UseWebLogin
$web = Get-PnPWeb
 #0 - Inherit, #1 - AllPages, #2 - ModernOnly, #3 - Hidden enums for Global (Modern Search)
$web.SearchBoxInNavBar=3
$web.Update()
Invoke-PnPQuery