So yes, the basic question:
Considering the tweaks in Legend of Zelda canon throughout the years, is it meant to be presumed that Link was [even retroactively] using the Master Sword as his strongest sword forms in the first two NES games?
This question is somewhat complex due to the nature of the retconning which took place over Zelda's 30+ year history. As these games were so early in the franchise, nothing could be explicitly said. Further complicating matters is that there is a lot which could be left up to interpretation in the series. To make searching for answers easier, I've assembled what facts here that I could from official game books, but any canon answer found outside of the manuals or comics would also be appreciated. That being said, here is what we know...
It is popularly held that the Legend of Zelda franchise has multiple timelines with re-incarnating Protagonists (Link, Zelda) and Antagonist (Gannondorf/ Ganon). The earliest games were simple and straightforward, without too much extensive back lore [The Triforce of Courage wasn't established, yet, neither how the Triforce of Wisdom and Power came to be, etc]. There was the basic story, with several details, as seen in the game manual here...
Even Link wasn't noted as the "Legendary Hero", yet; was just a random adventuring kid who had happened upon Zelda's servant, Impa...
The only mention to a powerful sword made in this game is the "magical sword", shown here. This, it would seem, would conclusively show that the Master Sword "wasn't a thing" in the first games...however, due to the ret-conning of the canon, that can't be held as fact. The "Magic sword" may have just been a simplified title to the "master sword", as they seem to have similar basic effects....
These basic effects are:
Increasing Link's striking power
Providing a magical based blade attack
Strongest possible offensive weapon for general use
The Lore got a little deeper in the next game, The Adventure of Link, where it was more or less established that Link was the bearer of a heretofore unseen Triforce, the Triforce of Courage.....
Again, however, even with the lore upgrade, it's never stated that this magical sword is precisely the Master Sword which becomes a lynch pin the in games history....
Canonically, the first specific appearance or even mention of the "Master Sword" comes in the SNES game Legend of Zelda: a Link to the Past ....
From here on out, the weapon becomes a MAJOR element in most of the games.
IT should also be noted that while the NES games call Link's sword "Magical", it bears no real physical resemblance to the Master Sword.
Now granted, I know on a practical level that during the NES years, the game's lore was still forming, so all elements may not have been set into place yet, much as how the third Triforce didn't "officially" become a thing until game 2. This would explain why the Triforce of courage is never mentioned in the American animated TV series...
Though this too is kind of odd, since the series came out in 88/89, and other elements from The Adventure of Link were used in there, but... whatever. That series was more of a "side tie in" rather than soemthing that arose directly from the video game lore, and it was prior to the first "official" mention of the Master Sword anyway....
This leaves us with 2 possibilities:
1. Those first LOZ adventures happened without the Master Sword, or
2. The Master Sword was there, but just mislabeled.
The first [and honestly, more likely] reason would be due to real-world issues; the story lore simply hadn't progressed to that level yet. This poses an in-story problem, though, in that the MS has been seen as a "key" element,almost to the same degree as the Triforce, so trying to "explain away" its absence would be difficult.
The second option is viable [and it wouldn't take much for any player to simply "accept" that the Magic sword, upgraded to its highest form, is simply the unnamed MS]... but then it sort of falls out of sync with the rest of the canon, as the MS usually has to be sought by the hero, in game; in most of the titles, it forms a sort of plot point, and its exclusion due to the MS basically "already being the hero's possession" kind of undermine's its import.
There is a third possibility, though....
Much like the Minish Cap is a crucial element in that particular game, but no other [The Master sword isn't even present, either, replaced instead by the "Picori Blade"] and the Wind Waker [arguably one of the most powerful magical tools in the LOZ world ] is hardly seen outside that specific game [not counting Twilight Princess and Hyrule warriors], the MS could just be of limited import in this timeline [since its established that the NES games are directly connected]. Certain items are given greater priority in given games/adventures/incarnation/timelines, after all.
And besides, these are different incarnations of Link, so this could just be a destined "absence". This feels less likely, however, as the import of the MS in destroying Ganon is pretty much stated throughout most of the canon, so it makes little sense that it wouldn't be so in the very first adventures.
Can anyone verify if this "magic sword" and the MS are one and the same?