Yea,
These types of missions can be a real pain for a GM to set up. You
really have to know your table, and what your players like to do. If you got a bunch of "meat potatoes" in the party, then you are almost sure that they will be bored and on their phones.
On the other hand, if you got a table filled with people who like puzzles... well, game on!
For me, when I DON'T know the table as well as I like, and I have to do this type of mission (Because hey, it does happen!), I try to plot it out on a sliding scale so I can tone it up or down to suit the interest I am seeing in the players. That way, if the players seem to be enjoying themselves playing "connect the dots" in the investigation I have laid out, then I can stretch it out. But on the other hand, if they seem bored, I can also cut it short.
For this, I usually try to structure the investigation around a NPC contact that can help me speed up or slow down the investigation through information, or action.
The key, as always, is to have to NPC be important enough to make sense for their role in the investigation, while at the same time not being a "Show-up" to the players. Thankfully there is usually a way to squeeze in such a person. (a family member of the missing person, the owner of the object, etc)
with out know exactly what is going on, its hard to help, but some general ideas:
If your group is enjoying themselves, then make sure you can throw in some Red Herrings to keep the investigation going... These can be anything and come from anywhere, so they are great to use, just don't over do it

Have a way to keep the players focused, and moving forward... Getting stuck, either through choice paralysis, or player ignorance leads to boredom and frustration. Have a way, to lead your players tot he next clue, even if it IS a giant red blinking arrow. Sometimes its needed.
Never assume a clue you have prepared is an obvious clue to lead to the next clue. some things are just not obvious to everyone. Sadly, I have generally found the knowledge gap between players and GMs to vary a great deal. So while you may think that by leaving shards of black glass at a crime scene is a great way to link Aztec to a crime; To the players, its a broken coke bottle. Hate to say it, but plan your adventure as if you are leading a 6 year around, and expect to solve your puzzle... That may sound condescending, but its easier to "smarten up" an investigation through removing some hand holds, then it is to "dumb down" an investigation your players a fumbling with (because now you are also fighting boredom and frustration).
Don't be afraid to throw in the towel and say "they went that-a-way!". Yea it sucks that your great investigation idea flopped... But now you have a chase!! Make the most of the situation and change things up. Make some notes of what went wrong, and learn from it for next time!
Keep in mind the general places players are to go for their Info, during an investigation:
The Matrix
Contacts
Fixers.
Those are the general 3 places most players go for their Info, so be ready for them to do matrix searches, or hound contacts for clues... that's what they are there for (so make sure you have things for those searches!)
Fixers, generally come in when the players just don't have any other ideas... so they look to "buy" answers. Or buy the skills to get the answers. Its good sign your players are either frustrated, bored, or just not into investigation work (They might be those Meat Potatoes I mentioned earlier!). If that's the case, then this is a good sign you need to rethink the clues and speed things up.