What Are The Symptoms Of Melatonin Deficiency?
No it shouldn't be hindering melatonin production.
Detailed Answer:
I read your question carefully and I understand your concern.
Pineal cysts are a common finding, in around 4% of MRI. They do not cause any symptoms unless they are big enough to compress brain structures. In your case those dimensions are considered small ones, which do not result in any compression which might affect the functioning of normal tissue.
So your cyst shouldn't be causing any alteration in melatonin production. There have been a couple of case reports where small cysts have been linked to low melatonin, but that's to little to generalize, there should have been more proven cases considering the frequency of the cysts. If there are really no other cause for insomnia is found a dosing of melatonin level could be done to put your mind at rest, but as I said there is no reason or scientific evidence to indicate these cysts can result in low melatonin when non-compressive.
I hope to have been of help.