It is a bit old question, but i get this question when i search for the same thing. After some reads, this is what i get. Hope it could help someone that search the same thing.
You could use the Client.getNumberId() function to check if the mobile phone number is registered on WhatsApp or not, check out the documentation on https://docs.wwebjs.dev/Client.html.
Note: you might need to sanitized the phone number first to ensure it is in the right format, which is , etc 618123456789.
61 is the country code, and the 08123456789 is the usual mobile number (remove the first zero on it).
var client = whatsAppWebClient.client;
var mobile_no = '+628123456789';
var sanitized_number = mobile_no.replace(/[^\d]/g, ''); // remove except number
// Get the registered WhatsApp ID for a number
var number_details = await client.getNumberId(sanitized_number);
if(number_details) {
console.log("Sending message to ", number_details);
/* send message */
} else {
console.log(sanitized_number, "Mobile no is not registered on Whatsapp")
}