Been there and done this many years ago, so I may not be completely up to date.
I was in a similar position to you, working for a company which made (still does make) high value low quantity systems.
When the "EMC Directive" was first brought into UK law, it fell to me to drag out equipment into compliance.
The route which we took was to do EMC compliance testing on the individual "modules" which were common to all systems, and then do some in house testing on a completed system in order to produce a "Technical Construction File" which presented our data to show compliance with the requirements of the directive. The TCF was then reviewed by a "Competent Body" and certified as good.
After that, all similar systems were built to the standard of the first system, and a TCF produced for each new system to show compliance with the requirements of the directive.
This must have happened about 20 years ago, much has changed since then, but the same general principle still applies I believe.
EMC compliance is about good engineering and not building crap, it is not to be feared.
EMC enforcement is, or at least was, complaint driven. So unless the system caused a problem, there would likely be no repercussions.
If there was complaint, if you could demonstrate that you had taken steps in your design to eliminate EMC problems you would not be going to jail, you would just be told quite firmly "Fix It!".
If however, you had been deliberately negligent, then fines and prison could result.
Having said all that, there is quite a bit of stuff like network powerline adapters and cheap PC power supplies which are an EMC nightmare and spew crap all over the RF spectrum, but enforcement is fairly laid back and not as rigorous as it could be.
JimB