Why would these merchants sail across unknown waters? Why not sail where there are certain oppurtunities close by?
In an alternate history where the Carthaginians overcome (or merely survive) Rome, I can see sailing technology developing much more rapidly than OTL as their sphere of influence focuses on mercantilism and control of trade rather than outright conquest. Trips to West Africa could very conceivably be blown by storm to South America, and with an abundance of timber it would be possible for the crew to fix the ship and sail home, bringing tales of the new land. I admit it's unlikely, but I don't think it's impossible.
To answer OP, Native Americans would not be better protected from disease; however, early and prolonged contact with Old World diseases from merchants would allow the populations to be exposed to diseases and recover from epidemics while said diseases become endemic. This would make it less likely that future conquerors will be able to use inadvertent biological weapons against the Native Americans. Plus, African mosquito-spread diseases becoming endemic to the Americas could protect Native Americans from European conquest. However, we will see cultural collapses as diseases spread and a lot of cultural shock from plagues.
Metal goods from Africa would be quite valuable for Native Americans, and coastal societies could become quite focused on obtaining these items, and eventually they may adopt metallurgy. Domestic animals from Africa could become adopted by Native Americans, which would open up savanna habitats in tropical South America to developing a much higher population fed by sheep and cattle.
The effect on Africa if cassava and maize is introduced this early will be massive. These crops were as transformative for Africa as the potato was for Europe, and we will see a population explosion south of the Sahara.