Hi @websavers,
We recommend following the steps in the PayPal Payments migration guide to ensure that subscription payments established via the now-deprecated PayPal modules continue to be processed: https://help.whmcs.com/m/troubleshooting/l/1782851-migrating-to-paypal-payments
If one did not follow those steps and instead deactivated the PayPal/PayPal Basic module, I've addressed your questions in-line:
Clients do not get a warning about this.
The company will receive the funds from PayPal, but it will not be recorded by WHMCS. A "Module Not Active" type error will be logged to the WHMCS System Log.
One could potentially add some instructions to this effect in the Invoice Created and/or Invoice Overdue Notice email templates.
It could also be conditional on there being a subscription ID present on the service record:
{if $invoice_subscription_id}
Follow these steps to migrate to the awesome new PayPal Payments gateway.
{/if}