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Though this surname is well known, thanks to Emil Zátopek, it is, apparently, very rare. This may be the reason that no one has bothered to furnish an explanation for it. Or it may be one whose origins can't be traced. Certainly the dictionary does not help.
Like you I've found dictionary words connected to 'flood' - zátopa, 'flooding'; zatopit (verb) 'to flood'. The -ek ending in Czech can be a diminutive or a surname ending.
One long shot is that Zátopek might identify the original bearer as someone living in a place subject to flooding, though I don't feel confident about that guess.