US Universities typically look at the last four years of academic performance. A few merits here and there, especially in the first 2 of those four years won’t matter much, but it really depends on how many merits there were, and if they were in subjects that are specific to your degree (e.g. Engineering Major won’t want too many merits in Maths, Physics etc.)
If you want to give specifics for better feedback, feel free to let us know

School grades are important in a US application for the last four years of school, but they’ll be happy as well to see that you’ve done some academic challenges outside of school which show your enjoyment and aptitude for the subjects you like most.
Strange facts 101: The Ivies mainly do it inhouse, but some schools like University of Miami will require you to send your grades from the last four years of school to an agency which converts your NCEA grades into an american GPA. So the colleges know how NCEA works, and which years are the most important (like in NCEA it heats up in Year 11/Level 1, but in Australia it tends to heat up in equivalent Year 12 and in the US it’s from Year 10).