If compliance is an important requirement, I would personally be careful with converting EML files into PDF as the primary archival format.
In that case, my preferred approach would be to archive the original EML files as-is, because the EML remains the native record and preserves the full email structure: headers, sender, recipients, subject, dates, MIME structure and attachments.
For example, with FileNet, it is perfectly possible to ingest and index this type of document by extracting the relevant email fields : From, To, Cc, Subject, Sent Date, ... and storing them as document metadata. This makes the emails searchable and governable without losing the original evidential value of the message.
The PDF can still be useful, but I would see it more as a rendition for consultation or sharing, not necessarily as the authoritative archived record.
In addition, IBM Content Navigator with Daeja View is able to display EML messages directly. ICN can also provide a PDF rendering on the fly when users need a more readable or portable view of the email.