I really don't know why I'm bothering with this, but here goes nothing.
Do we really need an icon for every ship buff we get? You either just get everything whether you need it or not or you know what you took. The important information is the remaining time on the buffs you took.
Why can't we have an option in the UI for just one icon that represents all ship buffs with a timer that starts when you take you first buff. All other ship buffs would not appear and would have their normal times. You would know that when your First Buff Timer was running out that the others were within one minute of expiring as well (assuming you didn't dawdle on the ship in-between altars/NPC's).
This would go a long way to clean up the buff icon bar at the top of the screen and make it easier to see quest buffs that can get lost in the mix.