I don't think they are trying to do a cover story.
However I do think they know considerably more than they are letting on.
By 'they' I mean 'a government' - not necessarily the Malaysian Government. The Malaysian government may/or may not know where the plane is.
If they DID know where the plane is, they may not want anyone to know for various reasons. Either because they are involved in someway or know it shows massive weaknesses in their own national security (For example if X country became aware that the plane flew their airspace, would they necessarily want the rest of the world to be aware of this? Its possible you have corrupt individuals or groups who allowed it to happen. This could provoke internal unrest or a political crisis AND an international one).
Also if they knew where the plane was - and it is on foreign soil - you have an issue. You have a bunch of hostages to consider. And who has the authority to do anything to get those hostages. There may be contact with the hijackers and negotiations going on. If there isn't contact, they wouldn't want to advertise they knew where it was for fear of what might happen whilst they created a plan. It would put power back in the hands of the hijackers rather than having the element of surprise. And of course you have several nation states involved - Malaysia, China, the country where the plane is and potentially other states who have passengers on the plane. Does the local authority take charge of a storming? Or does Malaysia? Or China? Or someone else? (Or do they have a diplomatic battle over this?) Depending on where the plane is, you also have to ask, would the local government even want to storm a plane and could they being obstructive.
And then there is the wider politics of it. If it IS somewhere like Iran, Afghanistan or Pakistan, then you have something of a problem IF someone is denying it or being obstructive. You can't just DO something on foreign soil, and even if you made it public, you could have an almighty mess on your hands. Something that could blow up to be far more than 239 missing people.
There are loads of reasons which aren't about conspiracies but are legitimate concerns as to why they wouldn't tell the media. They had to tell the media, the plane had been taken, as it was getting to the point that evidence was leaking too much from various sources that couldn't be controlled. At this point, it probably is easier to control any additional information that is known due to it being a more organised process and leaks in the midst of conspiracy theories aren't necessarily as obvious.
I've always taken the attitude of reading between the lines with media... I would watch the actions rather than the words of any country involved.
My inclination is that the plane didn't go in the sea though and do land. And I do think to a certain extent, we need to be open minded about things that we didn't previously think possible - especially since people with expertise keep going "well thats impossible" and then it suddenly becomes apparent, that yes, actually it is. (Weren't we all told a few days ago that cyber attack wasn't possible, then suddenly lots of other experts are saying "hmm well if they did this, then yeah actually it might be" for example).