It should be noted these files are blocked as they almost always contain malware. Typically, people will forward emails rather than attach an email as an attachment to an email, a very abnormal practice.
However, this can be changed. By default, the filter file is /etc/cpanel_exim_system_filter but you can verify if this is the case on your server by going to WHM -> Service Configuration -> Exim Configuration Editor and viewing the setting for "System Filter File."
In the default file, you will come across a line that looks like
Code:
if $header_content-type: matches "(?:file)?name=(\"[^\"]+\\\\.(?:ad[ep]|ba[st]|chm|cmd|com|cpl|crt|eml|exe|hlp|hta|in[fs]|isp|jse?|lnk|md[be]|ms[cipt]|pcd|pif|reg|scr|sct|shs|url|vb[se]|ws[fhc])\")"
Notice the eml in there? Properly removing it should allow .eml attachments through. However, realize that doing so is potentially a security risk to your users.