This is a good question and one that I've gotten a few times. The simple answer is, no, it isn't too overt, but please allow me to elaborate. One of the biggest challenges facing a GM when running an investigative mystery is understanding how much information to give. For the most part, everything will seem like too much because the GM already knows the whole plot thus leading to a tight fist on any information. This is not a fun game to play in because there is very little feedback for the players to tell them they're on the right track.
For those who have not seen the clue cards, here is the text in question:
Clue #1 of 4: What an odd rug
The geometric design on the rug in the library seems to match the design on the frame of the painting. Is there some connection?
The clue in question is given out automatically once the characters have seen both the carpet and the creepy painting (the frame of the painting has similar markings). You are correct in stating that the characters will likely just flip over the carpet and find the trap door... and this is a good thing! You WANT the players to do this. Remember, the secret areas do not solve the mystery at all. They merely lead to additional clues. The flipping of the carpet and locating the hidden areas will make the players feel like they've discovered something. This will make them feel invested and proud of their accomplishment. It will also drive the story forward.
Most GMs feel instinctively that they are here to defend the mystery as though it were an NPC in a fight. This is not the case. Consider the alternative: the players never think to flip the carpet and never discover the hidden areas. The characters might get to the end of the adventure, but they miss out on all sorts of great story material and understand a lot less of the plot. This is a tremendous waste and accomplishes less than nothing. The risks the characters face in the game shouldn't be that they miss the adventure. In fact you want to encourage them to explore everything you've prepped and reward them consistently for doing so. You also want to give them MORE than enough information so that they can form a clear idea of what is going on by the time the end of the adventure draws near. This is the job of the GM in an investigative adventure. If they solve the adventure quickly (which is not likely since placing stacks of undiscovered clue cards in front of them virtually guarantees that they'll feel driven to collect them all), then they almost certainly had fun doing so. The opposite is almost never true.
I hope that helps clarify things a bit.
Oh, In case you're wondering, yes, all of the undiscovered clue cards are left face down in plain view. They are sorted into their little piles (series A, series B, etc.) and left there so that the players can get a sense of how much there is to discover. Some players also take note of how many cards are left in a series, or how many series they haven't yet discovered. This is fine so long as they don't read the front of the cards (no one has yet tried to do this). This helps them feel they can gauge their progress in the investigation.