Hiding something does not equal a conspiracy theory. I mean, do you believe that behind every door there is a conspiracy? Do clothes equal a conspiracy to hide the human body? Is covering a seed with soil a conspiracy to hide seeds? If you think yes, than please tell us what you think a conspiracy is. Or are people just trying to protect property, keep warm and grow plants? Maybe they are conspiring to protect property with carpenters?
In this case, I think its reasonable to thing that covering up the ship and bodies are to protect dignity.
Hiding something does not equal a conspiracy theory. But it also doesn't refute it either. It cannot be used to comment on it at all.
Your clothes analogy is a straw man. People conspire all the time. There are many, many instances of people conspiring. There are many instances of conspiracy theories thought to be rubbish that turned out to be true. Watergate, anyone? Or more recently, if you had suggested that the NSA had tapped every major network in the world and created viruses that burrow down into the chips themselves and so on, you'd have been called a conspiracy theorist. Then came Edward Snowden.
Yes, covering with pebbles doesn't provide any evidence for a conspiracy theory. But equally your argument provides no refutation that it's a conspiracy.
Science however can offer concrete facts. For example: laboratory tests on debris recovered illegally from Estonia's bow yielded trace evidence of an explosion.
So how do you review that? By performing independent tests on other salvaged material. Which could be quite simple to do, if it wasn't covered in stones. Just think, if it wasn't covered in stones, you could recover some of the wreck, test it and show that there is no trace evidence of any explosions.
Now that we only have that trace evidence, I suppose we just have to be content with the idea that it was sunk with an explosion. Unless you have some kind of evidence that refutes it?
You may think the reverse, that this evidence cant be trusted, and that the official line should be trusted. But you would be wrong. That is unscientific. You would have to prove that the work done by Jutta Rabe is false by doing your own lab work and making your own observations.
Interesting how the pebbles stop all further investigation, isn't it? But I know, I know. Governments would never do that. They are so trustworthy. They never lie. etc. etc.
Good luck with your understanding of geopolitics, clothes and carpentry...