Living as creatures only an inch in height is difficult for the Clock family, as it is for all fellow Minish that dwell within the nooks and crannies of the castle they'd come to call home. While resources are prosperous, being found out is much more risky than it would have been anywhere else.
Not to mention, the scholar's apprentice was hell bent on finding and keeping them as test subjects.
And then really, considering all else, it wasn't that bad that the Princess' friend, who had a peculiar love for bugs, saw them as insects worthy of collecting.