First, historical background and airplanes
During WW2, bombers were an ESSENTIAL part of the war. Bombers were made to strike directly into the enemy territory's heart and you can repeat those bombing raids over and over again and weaken the territory (much like what happened to Berlin between 1940 and 1945).
There are different types of bombers:
-Light bombers: usually fast, small and with very little payload, they are made to fly directly into enemy territory and retreat quickly (only example I can think of is the Vautour, a french light jet bomber from the 50's)
-Dive bombers: typical light bombers that fly at high altitude then dive onto the target from above, only to release the (little amount of) payload and break off from the dive (for example the Helldivers)
-Front-line bombers: bombers that do not have many bombs and are meant to fly over enemy territory, drop the bombs, and fly back into friendly air (for example the Martin Maryland)
-Heavy bombers: bombers that carry quite a few (even a lot) of bombs and are meant to fly at high altitude and make large-scale bombing raids onto the enemy (for example the B-32)
Heavy bombers and front-line bombers are the ones that are usually vulnerable to enemy fighters as they are usually slow and not very maneuverable.
Now onto the dragons
The same logic would apply. Some dragon bombers would have different roles like the ones above. Fast and small dragons can be used as light bombers or dive bombers. 160
Slightly larger dragons as frontline bombers and large and heavy dragons as heavy bombers.
The two latter dragons need to be escorted by a group of small dragons that can play the role of fighter planes, and can defend the large beast from any enemy attacks by griphons or eagles. They would also need to be mounted with several men that also have bows and arrows or other projectiles, replacing the role of gunners that many heavy bombers in real life had.
According to what you stated, it seems that the Portuguese fleet does not have animals over 5 meters while the natives can have 30 meters long dragons. This gives the natives somewhat an advantage. Since at first the europeans needed to arrive to the Americas by ship, those ships can be obliterated by the heavy dragons that would need to fly very high and can raid the entire naval fleet.
One slight problem
If for instance your B-17 gets shot in the belly by any enemy aircraft (like a Bf-109 for example), the bomb bay door would be damaged with many holes and some hydraulic lines can be severed, but the bomber is still flyable and can be brought back to safety at the home base.
However here we have dragons which are animals not machine. So if a similar situation happened where enemy fighter creatures wound the dragon's belly for instance, it would be worse as it would bleed and be probably painfull, and it would be more difficult to bring back the dragon to home base as it would possibly be weakened. 160