Actually , we used the same backup to restore on both V10 & V11 , So the data on both the versions is same. After restore, we ran vacuum full analyze on both the servers .
default_statistics_target value "1000" is same on both the versions. Used the same postgresql.conf , i,e it is same on both V10 and V11
Hm. eqjoinsel didn't change at all between v10 and v11. Are you *sure* those installations have the same configurations? A plausible theory is that one has got a much larger default_statistics_target than the other (or at least, did when these tables were last analyzed), and in consequence these tables have large most-common-values statistics arrays, but not in the v10 installation.
[ thinks for a bit ] It seems possible that you could end up here even if the user-level settings are indeed the same, as a result of
which changed the method for deciding which values are MCVs. Maybe these tables have some corner-case distribution that causes the new method to think there are many more MCVs than the old one thought.
First thing to do is to look into pg_stats and see how large those arrays actually are in each case ...