TLDR: Look at the IdenTrust numbers if you want to know the real Let's Encrypt numbers.

Not many people use Let's Encrypt's own root for their validation chain when they use Let's Encrypt certificates. The Let's Encrypt root is not propagated widely enough across clients.

We (Let's Encrypt) have a cross-signature from IdenTrust, that's what most people use because it's widely trusted. IdenTrust issuance is otherwise very small, so you can effectively consider the IdenTrust numbers in charts like this to be a proxy for Let's Encrypt.

-Josh from Let's Encrypt