Question 1: If someone attacks his deck through his comm, is the deck really protected by the firewall rating of his comm, which is the device rating of the comm (6)?
You don't really attack "through" his comm in this edition. The attacker would attack the cyberdeck directly. The cyberdeck can take advantage of the firewall from the commlink it is slaved to. Attackers that gain a mark on the cyberdeck also gain a mark on the commlink.
(the cyberdeck icon can only be targeted if you are not using it as your cyberdeck icon will vanish and be replaced with your persona icon, so in this question i assumed the cyberdeck was just like any other random slaved device to a master device).
Now Bob wants to do some illegal activity. He decides to go into Hot-Sim VR. He boots his persona with his Deck in Attack 6, Sleaze 5, Data 4, and Firewall 3. The deck remains slaved to the comm.
Now you are using your cyberdeck with your persona and not as a stand alone slaved device. There might or might not be difference here. You can only slave devices to other devices or hosts. Since your persona is not slaved to the comm, i am not 100% sure your persona will use the comm firewall or the firewall attribute of your cyberdeck.
So the real question is if your persona get the comm firewall rating for the purpose of defense or the cyberdeck firewall rating for the purpose of defense (i think your persona icon would have the cyberdeck firewall rating, not the commlink firewall rating - even for the purpose of defense against matrix attacks. the persona is not slaved to the commlink).
Question 2: Can Bob use the data attribute of the comm (6) even though his persona is running on the Navigator which is currently set with a Data attribute of 4?
No. His persona is not running on the commlink. His persona attributes are equal to his cyberdeck. Slaved devices can never use the master device data attribute for anything. They can only use the firewall rating and only for defense when under attack.
Question 3: When he resists this Matrix damage, does he use the Firewall of the comm, or the deck?
You never use the master device firewall attribute for resisting matrix damage - only for defense tests to avoid attacks. He use the firewall attribute of his persona which is the same the current firewall attribute that his cyberdeck is configured for.
Question 4: Assuming he takes some Matrix damage, is the damage applied to the deck his persona is running on, or the master comm?
The damage is applied to his cyberdeck. Attacking a slaved device will never cause damage to the master device.