@kuya19
Let’s fix your example sentences first. We need the linker “na” for “huwag hayaan/payagan -> huwag NA hayaan/payagan” and “hayaan/payagan gawin -> hayaan/payagan NA gawin”. The sentences should therefore be:
Huwag moNG hayaan ang mga bata moNG gawin ‘yan.
Huwag moNG payagan ang mga bata moNG gawin ‘yan.
The answer given by @jkos is correct. The idea of “allowing” is common to both, but strictly speaking, they are not interchangeable because “hayaan (let it be)” is more about an event that has already begun while “payagan (give permission)” is more about an event that has yet to begin.
The event under “hayaan” could be ongoing at that moment (present tense) or a series of discrete, but identical, events that began in the past and are still expected to happen at present (present perfect progressive tense). Its relation to the “present” should be reflected in the verb it refers to such that the first sentence should have been:
Huwag mong HAYAAN ang mga bata mong GINAGAWA ‘yan. (They are doing it right now/They have also been doing it in the past.)
Conversely, since the event of “payagan” is yet to happen, the verb should be in the infinitive.
Huwag mong PAYAGAN ang mga bata mong GAWIN ‘yan. - Your example is correct.
We have a tendency though to use them interchangeably to mean “allow” and we just do the mental adjustments to get the intended meaning. Your two examples, with the “na” added, therefore, would actually sound just fine to us. In fact, even “Huwag mong PAYAGAN ang mga bata mong GINAGAWA ‘yan” is something you might hear some of us say.
Other variations:
1. We might also use “hinahayaan” or “pinapayagan” instead, which suggests that the person being told so has been allowing them to happen in the past. Though that assumption might be incorrect, it would still be understood in its proper context.
2. At times “bayaan” or “pabayaan” is used instead of “hayaan”.
Ergo, just be aware of the grammar rule, but don’t worry about deviating from it since we native speakers occasionally do it, too. 😅
Finally, just in case you used “mga bata” in your examples to mean “children”, that meaning changes when you add “mo” after it. In your given sentences, “mga bata mo” would be understood as “your underlings”. If you wanted to say “your children” it has to be “mga anak mo”.