As a general rule, the passage of time does not "cure" a zoning violation. A municipality typically has the right to require you to remove an unpermitted improvement, or require that you seek approval - and may seek back taxes.
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Generally, yes a County can require permitting after-the-fact even if the time period has been decades. If it was built illegally without permits, it remains illegal until permitted. I am not sure what you mean when you say you have "paid the penalty." If they fined you for failure to comply, then you still have to comply even if you paid the fine. If they charged you a fine, and allowed you to keep the structers then that may be a problem. You will need to retain a local attorney if you want to fight this.
While not recommended, it's not unusual to get permits after project completion. Permits are necessary, without them, the building department can take you to court and require you to remove any unpermitted construction. While this may seem burdensome to the property owner, keep in mind that the building department, its permits, and codes was initially instated to keep you and the public healthy and safe.
For your consideration, two things:
1) Do you have homeowner's insurance? Are they aware of the unpermitted structures? Heaven forbid you need to make a claim if someone were injured in/on one of these structures, you may run into difficulties getting the insurance company to pay for damages or medical costs incurred on anything unpermitted.
2) If you were to resell your property at some point, an appraiser may not include any unpermitted structures in valuing your home. So obtaining permits may add to your property value.
Regardless of the above points, you should consider bringing any unpermitted structures up to code for your own personal safety.
Best of luck in that endeavor.