After Moriah takes sailors shadows he puts them on a boat and sends them out to sea. But he says that if the person who the shadow came from dies the zombie they gave the shadow to will die. So why does Moriah send the originals back out to sea? Wouldn't it make more sense to just lock them up so they don't die? Otherwise their zombies would just keep dying.
To understand this situation we need a bit of context into Gecko Moriah. One of the Shichibukai, major antagonist of the Thriller Barque and the user of Kage Kage no Mi. His Devil Fruit power allowed him to manipulate shadows in a physical and tangible form.
Moriah maintains a very relaxed and laid back stance at all times. He rarely fights against his opponents directly, preferring to use his doppelman to outmaneuver them and then steal their shadow. (Luffy and Robin both lost this way). Or he may order his crew to take care of it. In general, he will avoid a conflict all together
His tendency to avoid conflicts shows how he collect shadows for his Zombie Crew. He ambushes pirates in the Florian Triangle, steals their shadows and leaves them adrift at sea. His crew of Abasolom and Perona also have powers of the kind which can defeat an opponent without fighting head on.
However, keeping the pirates whose shadows he has stolen would prove counter productive. One of the reasons Moriah was defeated was because of the pirates whose shadows he stole.
- Zombie's Weakness - Brook was able to discover the weakness of Moriah's Zombies because he was left on Thriller Bark
- Rebel Alliance - The survivors on Thriller Bark banded together and plotted to bring down Moriah. They understood his powers as well as stole over hundred shadows. They used the shadows to power up Luffy.
- Handicap - Due to a weakness to the sun, a Shadowless person would have a great handicap and once set adrift would not be able to search for Thriller Bark properly. However, due to extreme fog in the Florian Triangle, this weakness is negated somewhat.
Tl;Dr. There is a greater chance of Pirates rebelling and stealing their shadows back if they stay on Thriller Bark, rather than if they're sent away because of their instinct of Self preservation. It is also in line with Gecko Moriah's nature to avoid conflict until necessary.
Luffy is strong, probably the strongest shadow Moria caught, but we can all agree that if he went to sea alone and shadow-less he would die instantly. I think the best for Moria is to keep the originals prisoners in a Seastone prison, but keeping all of them is counter productive like you said and fodder shadows are easily replaced but general zombies are not.
Sanji had a 77 million bounty and he was made into that penguin but Zoro was 120 million and was made general zombie, so I think general zombies are all 100+ shadow bounties or just special bodies like Ryuma and maybe Captain John, etc, so it's better to capture these shadows in a Seastone prison and send the others. Having 20-50 prisoners isn't that bad.