As you mentioned yourself, the API does not currently support a filter operation against null values for said property. However, you can do the filter the other way around - use the NOT operator to exclude the two other possible values, namely "Accepted" and "PendingAcceptance". In other words, do this:
Get-MgUser -Filter "UserType eq 'Guest' and NOT(externalUserState eq 'PendingAcceptance') and NOT(externalUserState eq 'Accepted')" -ConsistencyLevel eventual -CountVariable count