Maybe only player-controlled characters are counted?

This used to be an exploit, allowing bases to be captured faster with bots, especially when there was no limit on the number of bots in a squad.

Maybe, but even on vanilla servers with players its very noticable

I found the end of the issue: SCR_CampaignSeizingComponent.c:RefreshSeizingTimer():270
When calculating deductions, m_iSeizingCharacters is 0, resulting in no reductions.

SCR_CampaignSeizingComponent.c:OnQueryFinished():179

if (prevailingFaction)
  curSeizingCharacters = Math.Min(totalFactionPresenceCount - curSeizingCharacters, m_iMaximumSeizingCharacters);

My interpretation of this code is that its supposed to calculate the X amount of players more than the defenders. Instead when a base is under total domination and being captured, it does: Y total - X attackers, so 0 players and 0 deductions when there are only attackers.

9 attackers, 0 defenders, 9-9 = 0

9 attackers, 5 defenders, 14-9 = 5

For the fix, at least in the short term, the value seizing attacker amount can be calculated as such:

SCR_CampaignSeizingComponent.c:RefreshSeizingTimer():179

if (prevailingFaction) {
    int contestingPresence = totalFactionPresenceCount - curSeizingCharacters;
    curSeizingCharacters = Math.Clamp(curSeizingCharacters - contestingPresence, 1, m_iMaximumSeizingCharacters);
}

@l909 ^

Fixed: Base capture speeding up depending on the number of people capturing was broken 

1.8.0.5 Changelog