When deleting a certificate, make sure that you have removed any references to it from your webserver configuration. Otherwise, your webserver won't be able to restart.
Indeed, you should not be manually deleting any files or directories under /etc/letsencrypt/. Once you do that, Certbot no longer understands how to interpret your commands.
Deletion should be done via certbot delete --cert-name <name>.
As yes, unless you believe somebody has stolen your private keys, there's no need for revocation.
@rg305 Your statement and link are not very useful (not at all to be exact). The quote about OCSP signing and HSM load does not mention the difference between a VALID or REVOKED OCSP status. The link you gave also doesn't make any distinction except for revoking possibly leading to a LOWER load.
@Osiris, I don't work for LE, so I can't say with complete certainty.
But I have heard it said over the years that you should NOT revoke a certificate without cause because it add an unnecessary load to the HSM.
Maybe someone more familiar with this can chime in... @schoen @jsha
It does add a little bit if you just count the amount of times the HSM has to sign anything:
1 signature for signing the certificate
10 signatures for OCSP (3 days lifetime) during the 90 day lifetime of the certificate
If you add a revocation, that OCSP response has to be signed immediately, so adds one to the already 11 signatures, making it 12.
For a sporadic revocation, that doesn't really matter on the 1.5+ millions of certificates issued per day, but an increase of 9 % load on the HSM if every certificate would be revoked during the lifetime of the certificate is a different story.
So personally, IMO revocation doesn't constitute a "very resource consuming action" if done in moderation.