Can high junior year grades overshadow freshmen year grades?

I’m currently a junior at this moment. My freshmen year wasn’t great especially for Harvard; my gpa was 3.0 UW ( I got all B’s in honors classes). But my sophomore year I got myself together and had a 3.8 UW in all honors. This year i’m taking 6 AP’s and most likely going to finish with a 4.0. Will Harvard look at it favorably that I improved tremendously and did well and in challenging courses? Not asking if i will get in but when considering my academic career, will harvard see it as suffice?

yes. improving your GPA, despite taking progressively more difficult classes, is important for admissions to competitive colleges.
but do yourself a favor when your Sr year comes- dont aim for only HYPS, etc level colleges. there will be tens of thousands of equally “qualified” applicants to those same colleges- all vying for a few spots.

Yes, it makes a difference. Whether H or any highly selective will just overlook those grades is a whole other story. If there is a good reason for this, explained by the GC, it could even be a positive thing. I know of a few such situations

But do bear in mind, that these very very selective schools get so many applications, are looking to cut, not to find reason to excuse. So what do you expect will happen when your gpa with lower freshman grades is in the mix with those kids who did well all 4 years?

Understand that the most selective schools are just that—most selective and like lottery tickets. Make sure you have schools where your gpa and other stats are very strong even with the lower grades freshman year.

Why are you interested in Harvard? I hope you continue to work hard- and not just to get in to college. Follow your interests, make good friends, enjoy high school. You will be able to find a school that fits you, rather than trying to fit yourself to a school.