Heat measures your squad's signature within the AO in Recon; a higher heat score basically leads to more prepared enemies. Since you are deploying in the enemy's backyard, high heat makes it much harder for you to conduct basic reconnaissance activities. Thus, it is in your own interest to keep your heat score as low as possible before deploying at each patrol.
What affects heat?
Killing enemies: At lower heat score, one enemy killed is one heat but this drops as the heat score rises.
Leaving rangers MIA: Every MIA soldier adds 5 heat to your score, regardless of if the soldier is healthy, wounded, or dead. Since you only get 1 Evac, make sure all your soldiers are ready to leave with the chopper.
Blowing up enemy supplies or assets: Each asset destroyed typically by C4 or Artillery gains you 5 extra heat and 1000 extra exp, generally not being worth the heat increase unless you want to increase your heat score for a more target rich environment.
Calling support: Support such as Fast Air or Cobra Gunships will increase your heat score by 1.
Time: Each day waited (skipped by clicking the calendar) can lower your heat score by 1 point per day. It is highly recommended to lower your heat score to a comfortable range before deploying.
Effect of heat
Heat heavily affects your ability to conduct reconnaissance. Primarily, it will increase the amount and quality of the enemies in your AO , as well as their resources: an AO that is mildly hot will have higher-ranked enemies including Main Force units, larger and/or more responsive QRF forces as well as greater enemy numbers in general. More heat will lead to an increase in Punji Sticks, Mines, and ambushes, as well as NVA units and Snipers. Rack up even more heat, and enemies will start to carry heavy support weapons, RPG's, and even mortars. Finally, if your heat is very high, you may even have to face NVA backed up with armor and a regiment (120-240) sized QRF that may deploy into the AO.
An AO with very little to no heat will have very few enemies, almost no traps, small, poorly equipped and slow to respond QRF and make for a very easy patrol. An AO with 50% or 75% heat will start to have enemies appear frequently, and close to the LZ. An AO with 100% heat is practically a suicide mission unless you and your men are very well prepared.