Also there are big reasons for not dumping upgrades onto a single ship. Flagship i could see putting 2-3 defensive perks to keep it alive, but i wouldnt go overboard. If a ship is destroyed, it becomes "scarred" and while having it happen once isnt that bad (you lose a defense token, or a squad starts with 1 less hp), if a scarred ship goes down the ship is removed from your fleet AND any upgrades that were on it go away.
The only time you risk losing upgrades is when you put them on a scarred ship. So, it's totally safe to stack upgrades on a single ship if you just take them off that ship when that ship becomes scarred.