Are ALL flares shuffled into the card deck no matter how many people play? There are a lot of flares and I am not sure if all of them should be included in the deck. Thanks for any info.

No. The two flares that each player is dealt are added to the deck. If there are fewer than five players, you add enough flares to the deck so that there are ten flares in the deck (eg. with three players you would add an additional four flares beyond the six that are dealt to the players).

Due to some miscommunication during setup, I once played a game in which all the flares were in the deck. We quickly realized the mistake but decided to play through anyway. You never know until you try, right?

Similarly, you never know whether conducting heart surgery on yourself with a rusty spoon is a bad idea until you try. But you can guess that it's a bad idea. Playing with all the flares is the same idea.