The water parks at Disney close one after the other during the winter season for refurbishment and upgrades. This is something that happens yearly, and is why they usually look clean and tidy and refreshed. It is still unknown (as far as I am aware) if the Shark Reef attraction at Typhoon Lagoon is closing or not - so this currently should only be taken as a rumor.
The Disney mini-golf is great fun, and definitely worth a visit if you decide to get the water parks and more package - we did the Winter Summerland course our past visit and really enjoyed it! But, yes I do agree with your comment about Disneyquest! Seaworld/Aquatica/Discovery Cove are great experiences - so if you do not want to experience TL or mini-golf, then they are definitely a nice alternative. The closures are something that comes with upgrades and expansions. Yes - It is a bit of a bummer that closures happen - but I am sure something great will replace it in the future.
If you definitely don't want to visit the Disney experinces covered by the 'water parks and more' package, take the opportunity to visit the other local Florida attractions - even if these are not the large companies like Uni and SeaWorld - there is plenty to do (we really enjoy the air boat rides). Have a fun and magical vacation!