Why does X-Plane 11 show the SR-71 at 200 knots but Mach 3 at 80,000 ft?
Indicated airspeed is derived from the measured total pressure and the static pressure, according to:

$$ V_i = \sqrt {\frac{2 \cdot (p_t - p_s)}{\rho_{SL}}} \tag{1}$$

At 80,000 feet, static pressure is 2761 Pa. Dynamic pressure as measured by a pitot tube, is measured after a supersonic shock wave according to the Rayleigh Pitot tube formula:

$$ \frac{p_t}{p_s} = \left[\frac{{(\gamma + 1)}^2 \cdot M^2}{4\cdot\gamma \cdot M^2 - 2(\gamma - 1)} \right]^{\gamma / (\gamma - 1)} \cdot \frac{1 - \gamma + 2\cdot \gamma \cdot M^2}{\gamma + 1} \tag{2}$$

with $\gamma = 1.4$ and M = 3, substituted in (2), gives $\frac{p_t}{p_s} $ = 12.06, so $$p_t = 12.06 * 2761 = 33\,290 ~\text{Pa}$$. Substitute this into (1) together with $\rho$ = 1.225 at sea level, and we get 

$$ V_i = \sqrt{\frac{2 \cdot (33,290 - 2761)}{1.225}} = 158 ~\text{m/s} = 307 ~\text{kts}$$

In the order of magnitude of what the X-plane indicated airspeed indicates, a lot closer than the TAS: speed of sound @ 80,000 ft = 298 m/s, Mach 3 = 894 m/s = 1,738 kts