https://xkcd.com/1342/ and http://www.explainxkcd.com/wiki/index.php/1342:_Ancient_Stars
https://xkcd.com/1440/ and http://www.explainxkcd.com/wiki/index.php/1440:_Geese
could it be that they are already black holes (the sufficiently large
ones) and we are just seeing the light emitted during it's main phase?
For some stars, yes it could be. There are certain stars that we can individually observe, and that we believe could go supernova more-or-less at any moment. Betelgeuse is probably the most famous example. It's 640 light years away, it could go type II supernova any time (expected within the next million years, but could conceivably happen within the next 640 years as we observe it, such that it's already happened). It might become a black hole when it does (although a mere neutron star is also on the cards, I believe, and probably more likely).
Furthermore, when we observe a distant galaxy it is certain (as far as our theories are concerned) that some of the stars contributing to the light from that galaxy have since become black holes. However, since we aren't resolving individual stars in those galaxies even with our best telescopes, you could have an argument whether we're "seeing" the stars or not.
is it safe to say that most of the stars are already dead that we see?
Stars in our galaxy, the Milky Way, no. It's only around 100k light years across, it contains 100 billion - 1 trillion stars, of which we can individually "see" only a small proportion. Most of those are very close, the furthest around 1500 light years, and most of those are not supernova candidates at all, let alone black hole candidates. Even allowing for our best telescopes, we still only resolve a small proportion of stars individually.
The galaxy probably experiences roughly one supernova every 50-100 years. So even if all of those were visible stars (which they aren't: even of the largest stars in the galaxy only a small proportion can be seen with the naked eye), and all the supernovae resulted in black holes (which they don't), then at most 15-30 naked-eye-visible stars could already be black holes, and only up to 1000-2000 total stars in the whole galaxy regardless of visibility are in the duration between going supernova, and earth entering the future light cone of that supernova. This extremely loose upper bound is by no means "most of the stars that we see", and in fact the chances are that none of the stars you see when you look up at the night sky are already black holes. It might well be that none of them ever will be.
It's also unlikely that any star you observe with the naked eye is dead, since their lifetimes are of the order of 10 million years (for the largest) to billions of years, and their distances from earth are 1500 light years or less. But there are a few stars, like Betelgeuse, that we know are near the ends of their life and that therefore might be "already dead" in this sense.
Using telescopes we can see some individual stars in nearby galaxies, or at least indirectly observe them since they're lighting up nebulae that we see, up to a few tens of millions of light years away (these tend to be blue supergiants, I think). Of these, those on course to turn into a black hole may well have lifetimes less than or equal to their distance from us. It's not necessarily the case that all or even most of them become black holes, I'm not sure what's typical of the types of star in question, but for those stars you can say that many or most are already black holes. The most distant individually-resolved stars are all dead one way or another.
If you allow for us "seeing" each star in a very distant galaxy, even though we can't resolve any of them individually before they supernova, then the numbers change again, but my instinct is that it's not the case that "most" of the observable universe is already collapsed into black holes. But the stars may well be dead even though they aren't black holes. We can see galaxies 10+ billion light years away, which is about the entire lifetime of a star like the Sun. To come up with "most", though, you have to firstly agree what counts as a star and secondly survey what kinds of star those galaxies contain. If you end up concluding that most stars are (by comparison with the Sun) tiny little red-brown things with lifetimes in the tens of billions of years, then most stars aren't already dead no matter how far away the galaxy they're in :-) On the other hand, the brighter objects that contribute most of what we observe via telescope in the most distant galaxies, sure, certainly die in far less than a few billion years.
Note that in special relativity the concept of "simultaneous" is a bit difficult to pin down. But I've followed the convention that if something is X light years away, then anything we observe from it between now and X years from now, has "already happened". We're not necessarily entitled from where we're standing to say that it's "already happened", since it's not in our past light cone, but good enough :-)