Skeleton Ship battles will indeed remain in the Sea of Thieves after the Cursed Sails event. Whether they’re there immediately afterwards, or a few updates later (like the return of the Megalodon’s children), we shall see. Senior Producer, Drew Stevens, re-re-re-confirmed this after being asked about it on Reddit:
We have these awesome server-wide Skeleton ship battles, of course we want to keep them! We’re working on how these exist in the emergent world along with the frequency of all our other threats, but expect to still be able to encounter these epic multi-wave sea battles.
Stevens also re-confirmed that cursed cannonballs will remain in the world as rare discoverable items – however, their effects be re-balanced before they arrive back in the world as usable items.
We are working to remove the stun lock element of these player-affecting curses and then do a further balance pass on effect timings. This work won’t land for the campaign [Cursed Sails] but will be in place for when they are found by players.
I’m confident we can reduce some of the frustration of these without removing the strategic advantage they will bring when in players hands (albeit significantly rarer to find).
I can’t wait to get my hands on some of these special balls.
Updated 17 August, 2018:
A minor update from Drew Stevens reiterating the above.
We’ve already taken feedback on the stun locking elements of the design and revised our implementation here. We’re looking forward to getting these into players hands and working to ensure they are balanced for PVP and PVE encounters. We’ll be reviewing the feedback from our Pioneers and during our next Adventure to see how they land and tweaking as necessary.