In modern cars, a bad thermostat can trigger the ‘check engine’ notification, it is this way because these mechanical valves now have electronic ties which make them part and parcel of your car’s entire engine management system.
With that said, why do mechanics suggest the complete removal of these crucial components even when they are not yet bad? What I will do in this article is to give you point blank reasons why they feel it is necessary to do this, but before that, here is a brief description of how they go about removing a typical thermostat and the consequences that follow:

As you might have noticed, radiator fans in new cars a thermostatically controlled, meaning they spin when the engine temperature requires them to (chances are that when your car is in swift motion your radiator fans don’t spin). Also, the device that switches radiator fans on or off in most cars is located within the thermostat housing, so when a typical thermostat is completely removed and not replaced, radiator fans don’t have that automatic factory on/off switch. A supposedly smart move by these mechanics to substitute for that switch is bypassing the pre-installed relays and connecting the fans directly to the battery; this can be akin to dismantling your domestic fan regulator and joining the positive and negative terminals of the wires to spin your fan. What this means is that whenever there is supply of electricity, the fan comes up; in the same manner in your car, so long the ignition is on and the battery supplies current, the radiator fans spins. With this in place, your engine can be over-cooled because water/coolant flows into the engine way too early and the continuously rotating fans are not helping matters at all. Another alarming truth is that with this arrangement in place, high voltage (12v) is being passed through low-resistance wires; you start wondering if those relays are for fancy for them to have by-passed it.

So now back to why mechanics do this, most thermostats are made of metallic springs which are quite prone to rusting. Also, because mechanics generally discourage the use coolants (which have anti-rust properties), they would rather have the thermostat removed as ordinary water quickly kills thermostats. So to put it in plain words, the underlying understanding behind taking out a thermostat is hinged on the belief that since most cars drive around without coolants, it is equally not necessary to use thermostats which you have to keep changing over a short frame of time.
This takes us back to the basics of taking care of your cooling system as earlier described in this article. Your car is your responsibility, take care of it.

source:http://www.autobaseafrica.com/why-mechanics-remove-car-thermostats/

The only reason i allowed the mechanic - with much insistence to remove my thermostat was the risk of the thermostat failing unnoticed. The effect i know is catastrophic.

My friend, who bought his 1st car(Golf 4) with no experience, damaged his engine within a month because of this or any other reason i don't know. I helped him take the car for checkup by scanning but found nothing wrong. The car would overheat and fan is still off or would come on for a minute then stop. While i know that when my car (Honda accord 97) overheats the fan remains on even after i switch off the ignition and lock the car. Fan relays were changed with no effect. I told his mechanic to just remove the thermostat he bluntly refused till the engine stopped in Kaduna Zaria expressway. He had to buy a new engine! The same problem started but immediately the thermostat was remove, fan was made constant then problem disappeared.

@ addany01 the thermostat is meant to allow the engine to operate at design temperature. Removal allows the engine to operate cooler than normal. This would allow the engine components to wear out over time and also increase consumption because the ecu won't disengage the choke. When I got my Lexus gs, It had overheating problems. My mech removed the thermostat. The engine temperature was always cold and i noticed the consumption was so high dat I averaged 10 miles to a gallon instead of the normal 18 for the car. The overheating problem stopped for a few days but it soon relapsed. I had to buy a double cell radiator ( it came with a single cell rad) and fix the fan to work all the time. The overheating stopped totally but the car was still literally drinking my fuel. I had to return the thermostat and now the consumption is back to normal. Our local mechanics don't know the essense of it that's why they order it's removal.