Saying it was because people abused it is just a misconception.
A classic example of community-made gossip which circulates out of control is accepted as truth shortly afterwards.
Players contrary to popular belief are not wholeheartedly evil + playing the game and using the mechanics is not bad behavior. (Read Kael's comments on the matter to get the picture of what is the teams stance.)
Also the FFH2-team is not! a defenseless, poor and clueless bunch open to abuse.
And last but not least in FFH2s case players are also playtesters right now. So players taking features to their limits and reporting the results is desirable, not problematic in any way (might! be if done after Ice is finished when the game is leaving beta or if not reported what the result is...).
It was changed mainly for the simple fact that the AI couldn't have been taught! how to use it (as opposed to: couldn't use it in the past or at present...) in any! sensible way or timeframe (as per comment from Kael.).
And that is a more serious and sound reason than any problems with balance could ever be. (since completely inept AI doesn't really mean quality or long-term fun to anyone unlike an unbalanced game which might appeal to some players more or less and isn't a problem for the AI by default...)
All other possible / percived problems if anything have been not the decisive ones.
If you do a bit of research on that one you can verify that all for yourselves in the bug-thread of the version prior to the change of pirate coves.
Otherwise i would agree with the OP and hope for the old coves coming back or some other way of meaningful terraforming of Land to Water for the Lanun.
But given above premise it just seems not a very good and sensible idea of use for the teams time...
(if any mod-modder would try I'm sure it would be appreciated by any Lanun players who whould like to not be limited to a rare few map-types.
But expect a lot of work if it is desirable to be accomplished in a good way. Including the AI being able to grasp it.)
I still think the Lanun have suffered quite a bit (in spite of the improvement to coves (which have imo unfortunately been nerfed again a bit shortly after improving them) and the implementation of Herons throne wonder...
Which btw. are a rather obvious sign that the old coves have not been completely unbalanced in the teams view either, otherwise some compensation for their axing wouldn't had to be put in.) but there seem to be many who disagree...
So quite a considerable part of the community seems to like the changes and be content+ with the new Lanun (which is surely what the team was aiming for so i have my doubts they would fiddle with it further. Given that Ice phase is growing closer at hasty pace...).
So its modmodders duty now if anything.
@ Blakmane: If I'm not utterly mistaken Tsunami was changed for the very same reason mainly (AI-ineptness in its use and coping with it + unreasonable time to get it to use it in a sensible way.) not so much it being unbalanced by default (Tier 3 spells need by rather extreme for them to be completely axed instead of reworked for balance-reasons. Read: meteor-swarm.).
On topic of citadels acting as cities, i for one think that a mini-modmod who does this (including it putting back their use at hooking up resources but! teaching the AI to not! use it on mana and for stationing their ships in them (or having it just hook up non-mana resources and the AI understanding it.) is badly needed.
I can very well understand the reasons why it isn't in the main mod though but can't picture them as very big problems for experienced players who opt that feature in.
But i am confident that something like this will come into being (even separated from other modmods which i hope, so it can be used separately or in combination with those at will...)
And with Ice fast approaching there is no big danger anymore that those modifications would be outdated anytime soon...
