What are the disadvantages of fitting underwing flaps to a Mirage III/5 fighter jets to lower landing speeds? The Mirage III / 5 series of fighter aircraft are versatile aircraft, but has a high approach speed of 180 knots and a high landing speed, requiring long runways.

Underwing flaps, like those of the Gloster Javelin, would surely work, and the fact that they are close to the CG would not cause an acceptable pitching moment. The tailless swept wing Messerschmitt P.1111 also had flaps on its trailing edge.

Gloster Javelin in landing configuration

Tested on a small free flight glider, I found that the flaps on a delta resulted in a noticeable increase in lift and decrease in turning radius, the elevons were not overwhelmed by the downward moment of the flaps. Using trailing edge flaps on a the same delta wing model resulted in an unacceptable downward pitch that could not be counteracted by the remaining set of elevons.

I would think the system would work, however my question is what sort of performance effects: increase in weight, for example, and possibly drag, would result.

Later models of Mirage incorporated canards and other devices to reduce landing speed did Dassault Aviation overlooked this option or did they evaluate it and decide that it would not be worth it?

I would have incorporated these in any delta wing fighter I designed, at least to offer it as an option to customers like the tailor made canards were to be offered.
Every airplane is a compromise of conflicting demands. While I am not intimately familiar with the Mirage family, I can easily see why flaps were never included.
In the early Fifties when work on deltas started at Dassault, the most important design parameter was top speed. High landing speeds were accepted, and given the design alternatives to a delta (think F-104), the landing speed could be considered low and another plus on the side of deltas.
When the first Mirage III were ordered, they had to serve in four different missions: As an advanced trainer (Mirage III B), an interceptor (Mirage III C), attack aircraft (Mirage III D and E) and for reconnaissance (Mirage III R). In order to allow for the widest variation in external loads, the lower wing should be free of flaps or other equipment which would restrict the attachment of tanks, armament or reconnaissance pods. Mounting any flaps at the straight trailing edge would require an opposite deflection of the elevons, negating any lift gain.
Flaps on naturally stable tailless aircraft are only helping if they are attached at a point ahead of the pitch trim flaps. This is possible with swept wings (see the Horten IX glider with its small flaps below) or with split flaps at mid-chord, like on the Gloster Javelin. With a straight trailing edge, no lift increase with a naturally stable configuration will be possible since the additional pitch moment of those flaps must be compensated at the same lengthwise location by the pitch control surfaces. What is gained with the flaps must be destroyed for pitch trim.

Horten IX V1 in tow, flaps lowered (picture source)
Since the Mirage line was never considered for use with aircraft carriers, its landing speed was accepted as part of the overall package. The Gloster Javelin was designed as a pure interceptor which put fewer demands on its lower wing. Also, the Javelin's tail helps to trim the aircraft in the landing configuration.
From the US translation of &quot;Aerodynamique de la Nouvelle Generation d'
Avions de Combat a Aile Delta&quot;, published in the AGARD Conference Proceedings No. 241:

Its [the Mirage III] aerodynamic formula, a delta wing swept back 60° at the leading edge, allowed Mach-2 flight with a single engine of 6 tonnes thrust, while its competitors were equipped with a 7-tonne J79.
The trade-off to this supersonic performance was a large increase
in the approach speed, 180 knots instead of 140 kt for the Mystere family. This constraint was accepted for the Mirage III, but later program specifications from the General Staff of the French Air Force required an approach speed below 150 kt.

So the Mirage III users had second thoughts, after all. The result of this lower approach speed requirement became the Mirage F-1.
Note that artificial stability allows to lower trailing edge flaps on a delta wing; the Mirage 2000 could be flown down to 100 kts airspeed.