As cautioned by New Horizons lead scientist Alan Stern last year, it's not so much that Pluto plays host to more small moons, the growing concern is for the potential clouds of dust and other small debris that the increasingly populated satellite system may generate.
"Even more worrisome than the possibility of many small moons themselves is the concern that these moons will generate debris rings, or even 3-D debris clouds around Pluto that could pose an impact hazard to New Horizons as it flies through the system at high speed," Stern said in a November 2011 mission update.
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As we spot more moons surrounding Pluto, the hazard becomes more acute, but the New Horizons team have a few tricks up their sleeve.
As discussed during a February Space Hangout with Alan Stern (video below), we were able to discuss some of the contingency plans, including aiming the New Horizons probe at Charon's orbit. The rationale is that Charon's gravity should clear a doughnut-shaped region around Pluto that will be relatively clear of dust and other debris, reducing the risk of a hyper-velocity impact with a hypothetical debris cloud.