We are aware of the performance issue due to the bigger cert informations.
I’m in favor of all your proposed options. In our case we will inform the customer about the negative performance effect. We issue certificates with accounts that don’t have a email address to avoid that LE is sending out emails to this accounts.
About the performance impact.* The more SAN names a certificate has the bigger the certificate gets. That’s a simple fact.
An average web page 2017 is about ~2.5MB . The cert size compared to the full web page is quite a small part.
For web pages we have HTTP/2, caching and CDN’s and other optimization techniques.
For the SSL/TLS handshake their are also techniques to reduce the overhead like session id and session tickets and the possibility to server a ECDSA cert. I don’t have any stats about the average ratio between full handshake and session resumption. For that reason I can not argue about the impact/gain of session ids/tickets. But my gut says session resumption save your ass even with a 500kB cert with approx. 25’00 SAN’s.
As a reference. cPanel**, one of the biggest web hosting control panel provider partnered with Comodo to provide free SSL certificates. Similar to ACME/Certbot their AutoSSL tool issues certificates.
The SAN domain limit is 200  for Comodo and obviously 100 for LE.
An increased of the limit would help us to reduce the burden to explain to our customers why some names are included in the cert and some not. Or to implement some opinionated sorting/exclude algorithms .
*This assumes that the certificate is mostly used to serving a web page. Their are other use cases like persistent connection like IMAP, SFTP where the handshake size compared the the rest of the data is most of the time only a small percentage of the overall traffic.
** We use cPanel as a web hosting control panel but implemented our own LE integration.