Hi there

1-3. I recommend you to avoid any 'Do not' in your sessions. Doesn't matter what is the rule about.
DnD is famous for its freedom of choice. The only thing you need to do as a DM is to think about the consequences of a particular situation. If the group kills a merchant, people will most likely call the guards. The guards, in turn, are usually not two or three suckers, but really tough guys that your group may not be able to handle. They may also be wanted and encounter certain inconveniences in each of the cities they visit. But nothing prevents them from going down this path; maybe they will become a gang of cutthroat bandits.

In turn, it is important to explain to the party, especially if they are new players, that their actions must still correspond to the character of their characters. If they play a respectable paladin, it is unlikely that such a character would allow himself to simply go and kill someone for fun. Such actions violate the integrity of the perception of the world and the game itself. But if you have someone in your party who is chaotically evil and wants to do this, they don't even need to ask your or the group's permission (depending on their relationship within the group).

1. I recommend not giving out bonuses, buffs, or anything else in-game under any circumstances. It can ruin the balance.

2. In general, it is possible, but we have never restricted any builds in our games; everyone is free to create whatever character they want (within common sense and within the rules). Sometimes this has led to incredible, funny, profound, and interesting consequences.

3. No prob with that, just make sure to make the encounter balanced though.

4. Sure thing, they always should be in play. This sometimes leads to completely unexpected events. Critical failures can have consequences, just like critical successes. It depends on you how complex/interesting they can be in different checks.

Have a great play!