It isn't usually an issue because most experiments are simply concerned with finding exoplanets. They are rarely designed in such a way that it is easy to estimate population statistics because of all sorts of biases that go into selecting the targets. Unfortunately the search for exoplanets has turned into a sport where discovery is everything.
If one assumes random orientation of orbits (and that is all it is, an assumption) then the probability of a transit scales roughly as
$$P \simeq \frac{R_p+ R_s}{a}$$
where $R_p$ and $R_s$ are the radius of the planet and hot star respectively and $a$ the planet's orbital radius (with small modifications for non-circular orbits). The larger this is, the more likely a transit is to occur. Hence large exoplanets orbiting close to large stars are more likely to transit. In principle then, this effect can be corrected for when calculating the statistics and frequency of exoplanets.
So how good is the random orbital inclination assumption? I honestly think nobody knows at the moment. I have done work on the possible alignment of spin axes within the low-mass stars of clusters (Jackson & Jeffries 2010) finding consistency with the random hypothesis. More recent work using asteroseismology suggests that there may be alignment for more massive stars (Corsaro et al. 2017). However, even if the spin axes (and therefore presumably the majority of planet orbits) of stars in clusters line up, there is no obvious reason why each cluster should have the same angular momentum vector When the clusters eventually disperse into the field then they would, presumably, form a pseudo-random distribution?
Except, what if the Galactic tides or a large-scale Galactic magnetic field played a role in shaping the angular momentum direction of the clouds that formed the clusters. Might it be possible for some alignment to persist to old age? Corsaro et al. argue that interactions within a cluster are not sufficient to "scramble" the angular momenta after star formation has finished. Close interactions between stars become much less likely after they emerge from a cluster into the field. An intriguing piece of work by Rees & Zijlstra (2013) found that there was evidence for a non-random distribution of orientation for bipolar planetary nebulae towards the Galactic bulge. This suggested that the orbital angular momenta of binary systems responsible for the bipolar shape of the nebulae were oriented in the Galactic plane. The result is highly statistically significant but as far as I know has not been followed up despite its obvious implications for estimations of transit yields from exoplanetary surveys.
I think that there will be a much better answer to this question once we have all-sky exoplanet searches of the quality of the Kepler satellite (the main Kepler survey was in one particular direction). It should become very obvious if there are changes in the planet yields as a function of position of the sky (although you also have to control for the types of star being observed) associated with any large-scale alignment. Maybe there is enough information in the Kepler K2 fields that are taken at positions around the ecliptic - I have not seen any analysis. However, such data will surely become available with the launch of NASA's all-sky TESS satellite in 2018.
