Also see bug 4190.
Fractional seconds should be hidden if the table definition did not specify that they should be stored. Specifically, N digits should be shown (and be editable in the timepicker) where N is the number for that field in the definition.
But in MySQL before 5.6.4, fractional seconds are not even supported for most data types. phpMyAdmin however still displays .000000 after every value, for e.g. TIMESTAMPs.
Please note that the default, when omiting N in the definition, is 0 in MySQL (since 5.6.4), whereas the default is 6 in standard SQL.
So for backwards compatibility, they should really be hidden. People that didn't update their MySQL are suddenly seeing all those zeros, while they can't even be stored (in their current definition) anyway.