The main reasons are mainly twofold:

• Their contact with the native people in Newfoundland/ Labrador was (probably deliberately) fairly limited, as I explained in [Were any diseases brought to America by the Vikings?] (https://www.reddit.com/r/AskHistorians/comments/arja44/were_any_diseases_brought_to_america_by_the/). Neither was there no traced remain of any not so small-scale material culture in ca. 1000 near L'Anse aux Meadows.
• The Norse people came to the New World around ca. 1000 did not entirely have the same set of the pathogens or immunity with those who colonized in the Central and Southern America in the 16th century. It is famous that the small pox devastated the population of Iceland when it firstly arrived there, a kind of virgin soil of this disease, in 1241, though I have failed to identify the sources on how much people died in its first outbreak. Anyway, it also means that the first Norse settle landed in L'Anse aux Meadows almost certainly [corrected] did not bring at least this deadly disease with themselves, as illustrated by /u/Reedstilt in If the Vikings visited North America before 1492, was there any evidence that any population was wiped out (partially or otherwise) by small pox?.