Background: PCs know enemies are in a room. Enemies are unaware of PCs and not even ready for combat (playing cards, cooking, arguing, etc). PCs decide to burst into the room and attack suddenly, like a SEAL team. Not using stealth, so technically no surprise.
No.
If the PCs are operating "like a SEAL team", then they should be making Stealth checks. If they don't make such checks, or they fail those checks, then they are making sufficient noise for those inside the room to hear them, and you should proceed with an initiative check as normal.
Question 1: Do you penalize the enemies on their initiative check (disadvantage), or give the PCs advantage, or neither? If giving advantage or disadvantage, do you roll two d20’s (DM discretion, PHB page 173), or add or subtract 5 (or some other number) to the roll (similar to passive perception checks (PHB page 177)?
As I said above, neither. In answer to the second part of your question, though, when (dis)advantage applies, you roll two d20s. The exception is when using passive Perception, but that doesn't apply here.
Question 2: Would you set the PCs up in the room, or outside?
Outside.
Question 3: Assume the enemies get the highest initiative roll. Do you allow them to get in the first round of attacks?
Yes. Be it because the PCs made a noise, sheer random chance, or because the opponent is a twitchy sod, he somehow gets to his weapon first. That is, after all, what winning initiative means!
Question 4: Would your answers change if the enemies were unaware but more alert and prepared, such as on guard duty?
No. The enemies being on guard duty may make it harder to gain surprise against them, but given that the scenario as described explicitly rules out surprise here, that doesn't apply.
It does help differentiate different levels of enemy awareness and alertness.
I tend to agree that it's a weakness that the game doesn't really differentiate levels of awareness.
However, virtually all adventuring takes place in hostile environments - the PCs find themselves raiding dangerous tombs, they face bandits in their lairs, they adventure in a wilderness filled with perils, and so on. So, outside of some acknowledged "home base" it makes sense that they would keep their wits about them - even when 'unprepared' they're still alert to the possibility of danger.
And what applies to the PCs applies to their enemies as well. They might be among 'friends', but they're still in an environment where an attack can come at any time - from the PCs, from a rival gang... heck, from the guy across the table who might have seen that card getting palmed.