In four stroke engines, spark occurs twice in one complete cycle i.e. at compression TDC and exhaust TDC (In some vehicles, there is a MAP sensor to identify the compression TDC. In such vehicles wasted spark can be avoided). Is there any disadvantage of this wasted spark? Does emission gases get affected by this spark? There is some overlap angle in which both inlet and outlet valves are open so if the spark occurs in this interval will it burn the fuel entering the combustion chamber?
From a theoretical perspective:
Is there any disadvantage of this wasted spark?
Depends on the ignition timing.
If the intake valve is closed when the spark occurs there is no risk of preignition.
If however the intake valve is open enough during wasted spark ignition that air and fuel reach the immediate vicinity of the spark plug, you run the risk of preignition which can lead to premature engine failure.
Does emission gases get affected by this spark?
If the engine is running too lean, practically all of the fuel has been consumed.
If it is running too rich, there is no air left in the exhaust gases to enable combustion.
There is some overlap angle in which both inlet and outlet valves are open so if the spark occurs in this interval will it burn the fuel entering the combustion chamber?
As explained above, only if the air-fuel mixture reaches the area immediately surrounding the spark plug.
I think you miss understand the reason for waste spark.
The example you give of a single cylinder engine puts you in the realm of lawn and garden equipment. 90% or more of such engines use a magneto style ignitions. Because the flywheel spins at the same speed as the crank shaft these engines fire the spark plug both on compression and exhaust. It's not that they are specifically designed this way, it's that they simply can't help it.
In the case of the 10% that are actually fully computerized, they are more of an abnormality than a rule. Because the cost of the electronics is high compared to the actual gains that such one cylinder engines would see the electronics are often sub par compared to their bigger automotive cousins.
To have a real discussion about waste spark you must discuss multi cylinder engines.
Finally, ignition does not occur at TDC, EVER. Ignition occurs before TDC, usually 10 to 15 degrees base timing. When the timing advance gets done with it ignition can go as high as 30 to 45 degrees before TDC. This pulls the spark event away from any overlap in the valve train.