Comment # 2 on bug 1023552 from Ludwig Nussel

There is no generic answer as it depends on the service. apache for example is
setup to have certs in /etc/apache2/ssl.crt/. Most services allow configurable
paths so you can put them wherever you want.

/etc/ssl/certs is not a directory but a symlink to /var/lib/ca-certificates/pem
nowadays, so hands off for the admin.