It definitely has a big effect of colonization, most especially Spain and Portugal. Spain definitely winds up with fewer, smaller colonies and the overall pace is much slower, ditto Portugal. Spanish influence is reduced overall and they and Portgual likely don't sign the Treaty of Tordesillas, splitting South America. It's possible some other countries might establish more South American colonies with a vacuum between sparse colonies, perhaps France, England, etc.
The generally slower spread of European settlers could potentially mean that European diseases spread more slowly and lower density of natives would further slow the spread. Some natives might potentially have developed some immunity by more gradual exposure.
I don't see how this would affect Portugal, since the part that they colonized didn't have any cities nor anything of the sort, just several agricultural peoples. Portugal didn't discovered Brazilan mines till the XVIII century, and I don't see why they may not do this IITL.
Concerning Spain, colonizations may be delayed, and les Spanish conquerors might come if there are no stories of success as the ones of Cortes or Pizarro. Yet we must remember that colonisation started before civilizations were found. The Caribbean and Darien were settled when only people living in small agricultural villages with a fea gold ornaments were found. And yet the Spanish settled. That trend might have continued, till they are sure there's nothing else. And by then a significant part of the continent might be settled... maybe not as much as IOTL, but stil something significant.
As long as there is an agricultural people that produce a surpluss, as were the Taino in the Carribean, the Guarani in Paraguay ot the Huarpe in Mendoza (Cenret-West of Argentina), the Spanish mode of colonization can work. Where it doesn't work is when you have Hunter-gatherers Nomads that don't produce a food surpluss and can simply move inland when the Spanish come. That's why Buenos aires was abandoned the first time after 1540, and why Uruguay wasn't settled till the XVIII century, despite having great land for agriculture: there weren't native workers, and the Spanish who came weren't interested in agricultural tasks.
Less Spanish would probably come if there are no stories of success (from the point of viwe of the conquerors) as the ones of pizarro. But those few who come, and the descendats of those who were already in the Carribbean IOTL before civilizations were discovered, mibht still settle in most of where they did IOTL as long as there are agricultural peoples.
Of course, if few Spanish come, and there are less centralized societies, there might be more resistance, and the Spanish presence might be reduced. Areas that IOTL where the focus of great native resistance that eventually failed, such as the Quilmes revelion in OTL Northwestern Argentina, might have succedded in TTL, reducing the Spanish presence to the Caribean, Central America, and a few strongholds in South America