Who/what has destroyed Winterhold? How and when? The local jarl Q.Q a lot about this event but does not give historically precise details.
Some NPC say the city was swallowed by the sea. A tsunami in The Red Year?? I couldn't find the ruins except the fallen stones from the bridge.
Some houses have collapsed. Daedra siege machines? Mages nuked the area? Why don't they rebuild it? Where can I find information?

have you tried going to the town and asking around?

Consoles destroyed Winterhold...

Yupp, ofc. But those are just regular mage haters [being a Nord I hate mages/magick too XD] and these conversations are like "Ahh yeah, you know the sea ate half of our city and we don't have any evidence but we know the mages did it somehow!"

Well, I guess you're right. You can't possibly have missed anything at all in the town, maybe near the northern part, possibly near a bridge that leads to the mages' college where I guess you may find answers. After all, what do I know.

Read the in game book, On the Great Collapse.

There is a line in the book about Shalidor that says one legend surrounding him involved him building part of the city of Winterhold... Which could mean the college... or does it mean he caused much of the land that was there to be there? And some how his magic gave out and the part of the ground fell back into the sea? Or is it just a way to explain what happened to the city?

We may never know!

They blame the mages because half the city fell into the ocean but somehow the ground the college was on stayed intact and still standing, that is why the college is set on top a narrow piller of land.

Winterhold was destroyed when the cliff gave way.
Some blame the mages college.

If anything Helgen is Kvtach.
A once great thriving community, attacked and in ruins, never to be rebuilt.

Well Bandits Live in it know Atleast

Why is Winterhold the way it is? Because the citizens there are too busy whining about how the mages did it without any evidence to support that accusation to bother with any attempt to rebuild.

Pretty much the only Stormcloak town that isn't better off with a pro-Imperial ruler is Riften... and nothing really changed there except the formality of Maven's rule; it was http://tvtropes.org/pmwiki/pmwiki.php/Main/IOwnThisTown to begin with...

No one rebuilds the small handful of destroyed houses because it seems like a hopeless cause. The majority of the entire city fell into the sea and now no one wants to go there anymore.

Helgen is Kvatch 2.

If you join the college you get a brief history lesson on how the town got demolished, but nothing to indepth

I wish they would try to rebuild it...

However, Helgen's fires do go out. And then the town becomes a bandit cesspit on account of being a ghost town.

If anything has Kvatch syndrome, it's the two demolished houses in Whiterun after the civil war battle. One dude dies in his house, the other is the house of that crazy Talos preacher.

From what I've heard/read & remember about the event, it sounds like a tsunami caused by the eruption of Red Mountain and/or the impact of the Ministry of Truth into Vivec City, which is said to have caused the eruption.

We really don't know what the seafloor looks like around Skyrim and mainland Morrowind. I do know that something about the seafloor west of Washington State tends to nullify or quell tsunamis; while California got about 10 feet, Washington got maybe a few inches of sea level rise, after the Japanese quakes.