The point is to not store them in plaintext.
That is probably pretty much it. As D.W. pointed out in his comments, that Benoit's answer, tells you their reason why they store phone numbers and that they hash them. ProtonMail does not tell you why they hash them. We all can only speculate about this, until an employee of ProtonMail tells us the exact reason.
The most probable reason is (in my opinion) is the following:
ProtonMail is a company whose whole business model is founded on secure products and protecting a customer's privacy. If they told you, that they saved phone numbers in plaintext, that would be pretty weird. Hashing them makes much more sense in that regard, don't you think?
On the other hand, ProtonMail doesn't link phone number hashes to user profiles, they flush the hashes regularly and as you stated yourself, there's not much to gain from a phone number.
Hashing phone numbers if they have to store them is better than not hashing them. That's why they do it.
Does it strengthen security much? No.
Is it better than storing them in plaintext? Yes.