I recall at least two references in Star Trek: Voyager where a Borg cube was severely damaged or completely destroyed by an ion storm.
The Borg are probably the most technologically advanced species in the Star Trek universe. They possess such powerful technologies, like trans-warp travel and assimilation sting, that can't be stopped or blocked by anything. They've collected (assimilated) the technological knowledge of hundreds, if not thousands of technologically-advanced species.
How can it be that the same species is unable to create anything to stop, prevent or at least warn them of something as simple like an ion storm?