This problem isn't unique to Let's Encrypt. Let's Encrypt is not the only entity with certificates signed by DST Root X3. And as these devices get older, more root certificates will expire. What happens when all of them expire?
What is unique about Let's Encrypt, is they may have a harder time getting cross-signed by a CA that will still have a valid root cert on these devices for a significant amount of time, because, as has been pointed out in other comments, Let's Encrypt is disrupting the CA industry.
But this is not up to Let's Encrypt to solve. They market themselves to build products for the mass market instead of small niches of the market, say, everyone who buys a new phone every year. But then they also have to treat their product like a mass market product, and if Android users still use older versions of the OS, then Let's Encrypt should adopt for that.