Feeling your heartbeat at night can be very scary. It sounds like you’re pretty fit and healthy. It would be very rare, indeed, for palpitations at night to turn out to be something dangerous or worrisome. Symptoms to be concerned about would be fainting (syncope) or a very rapid heartbeat associated with feeling lightheaded.
If you have a normal physical exam, good exercise tolerance and a normal EKG, it would be very unlikely to have structural heart disease (a weak or too thick heart, or a valve problem). An echocardiogram could be obtained, if there is any concern about the potential for you having a structural problem with your heart.
The important thing would be to correlate your symptoms with your heart rhythm. If you have symptoms every night, the Holter monitor should have picked it up. If you didn’t have any symptoms the night you were being monitored, then an event monitor or another Holter monitor would be in order.
Generally, symptoms like yours are from extra beats (PVCs or PACs, premature ventricular or atrial contractions) which cause some pauses and strong heartbeats. Everyone has them, but not everyone feels them.
I myself am very sensitive and aware of irregularities in my heartbeat. I understand the feeling, but I know it isn’t dangerous. Sometimes symptoms are from just a strong normal heartbeat (which can occasionally be caused by an overactive thyroid), and there are a variety of different types of rapid heartbeats that can cause symptoms and can be suppressed, if needed.
I worry that you feel exhausted. Sleep disorders, metabolic problems such as anemia or thyroid problems, need to be ruled out. Work with your healthcare team. You will get to the bottom of this problem.