Is there any reason not to keep fruits inside nalewka for too long?

Aging time is one factor that you might consider, but the amount of fruit you're using, how it's prepared, and other factors can have an impact too.

You're correct that the seeds and kernels of stone fruits can produce harmful substances, namely cyanide. More properly, they contain amygdalin, which is readily extracted from the kernels by ethanol. This substance can be broken down by enzymes (either those in the fruit, or in your intestinal tract) to produce glucose and hydrogen cyanide. To be fair, there are plenty of other common foodstuffs that contain minute amounts of cyanide precursors, but cooking generally renders them safe.

Cyanide is obviously very lethal, and there is real risk to consuming raw stone fruit pits. In general, the amounts required are fairly high, depending somewhat on the specific fruit. Somewhere between 13-15 peach pits, 17-20 apricot pits, or a full cup of apple seeds is enough to cause cyanide poisoning, assuming that you really wanted to choke down raw peach pits. Because of their smaller body mass, these amounts can be lower for children. Distilled alcoholic beverages are also a particular concern because harmful substances can be concentrated in the distillate. Peach brandy made by crushing and fermenting whole peaches (including the pits) was a popular liquor in the colonial-era United States (fun fact: even its first president tried his hand at some) but fell out of favor after it was implicated in multiple deaths. Modern producers of the plum brandy slivovitz also run the risk of creating cyanide in their finished product, but fortunately there are means of neutralizing and removing the toxin during distillation by adding copper sulphate.

Now that you're sufficiently terrified, here are some mitigating factors.

1. I can't find reliable information on the amygdalin content of cornus mas. They may contain a fair amount, or very little. They seem to be used in a wide variety of different preparations, so it seems unlikely that they're particularly toxic; otherwise a cultural aversion to them would probably have developed.
2. The enzymes that break down amygdalin into cyanide work most actively when the pit is crushed, so how you're preparing the fruit is a big factor. If they're left whole or only lightly crushed, the alcohol has relatively little surface area to contact and won't be able to extract as much amygdalin. If the pit remains undamaged, then the enzymes that would convert amygdalin to cyanide would remain mostly unactivated.
3. This isn't a distilled preparation, it's an infusion. At most, you'd be able to extract as much amygdalin as is present in the fruit - which could still be hazardous, but isn't being concentrated further.

If there is extended contact between crushed pits and the alcohol, then macerating for longer than instructed could be problematic. But in that case, the hazardous substance is already being extracted, and the original recipe could already make you sick if consumed in sufficient quantity. A potential fix for this would be to remove the seeds, but from your question I'm assuming that they're already included in the recipe.

In general, I'd say there's more to worry about here than over-infusing the fruit. if you've made this before and consumed it without adverse effects, then letting the fruit extract for longer in your next batch will probably not kill you. But be aware (and if you're giving this away, be sure the recipients are aware!) that there may be a small amount of hazardous substance in the end product. Overconsumption could indeed make you very sick (over and above the potential problems with too much alcohol) and the only way to be completely safe is to not drink it at all.

That said, there are measured risks involved in consuming many types of food and drink, from undercooked meat to homemade preserves. If you're preparing this for your own use, and you're aware of the risks, then it's your body and your health, and you can make your own decisions regarding risk.