My suggestion was just to deduplicate servers in individual DNS responses, not to disable them permanently in the pool. For example, if an NTP client is resolving 0.pool.ntp.org on start in order to get four NTP servers, it shouldn't end up with just two servers, one having three votes in the source selection algorithm, and the other having just one vote.
However, I think it's actually a good question whether pool members should be able to increase traffic to their servers by adding multiple addresses. NTP clients are a finite resource. If I add multiple addresses of the same server to the pool, other servers in the zone wil get fewer clients, right? Maybe it would help if there was an easier way to get traffic from zones where the number of servers is too small.