To quote from Batygin and Brown (2016)
Trujillo & Sheppard (2014) point out that the Kozai mechanism allows libration about both ω = 0 as well as ω = 180, and the lack of ω ~ 180 objects suggests that some additional process originally caused the objects to obtain ω ~ 0. To this end, they invoke a strong stellar encounter to generate the desired configuration. Recent work (Jílková et al. 2015) shows how such an encounter could, in principle, lead to initial conditions that would be compatible with this narrative. Perhaps a greater difficulty lies in that the dynamical effects of such a massive perturber might have already been visible in the inner solar system.
So the short answer is that it is unlikely a single encounter with a massive object could cause the perturbations without leaving other traces in the dynamics of the solar system. Furthermore, stellar encounters are rare enough as it is - encounters with black holes should be even rarer since stellar evolution and the critical mass requirement of black hole formation dictate there should be far fewer black holes than stars in existence.
To me that means favoring an encounter with a black hole to be responsible for the "unexpected clustering in their respective arguments of perihelion" of Kuiper belt objects over other theories would be a violation of Ockham's Razor.
All that being said, due to the chaotic nature of orbital dynamics and the relatively short Lyapunov time of Mercury in particular, it is very difficult to rule something like that out. It may be the case that an encounter occurred long enough ago that the only remnant is in the perturbations of long-period Kuiper Belt objects. And that all other traces of its influence on the inner solar system have been obscured by its characteristic emptiness - it could in fact have even been the cause of that unusual emptiness.
It should be noted of course that this would not have been a 'small black hole' (also sometimes referred to as micro black holes) as has recently been theorized in place of a 9th planet, but a stellar black hole (roughly 5 or more times as massive as our sun).