Given that the mines are certainly there, especially around the old so-called Baltic States governed by the Soviet Union, including East Germany (whose main port along the Baltic is Rostock) and Poland, it is something you might expect the JAIC to have ruled out?
Do you know how much unexploded ordnance (mostly a legacy from the WWII era) there is strung across the mouth of the Skagerrak between Norway and Denmark? Well, it lights up a map in a manner far more extreme than anywhere else in the Baltic Sea.
Now, the Skagerrak - being the relatively narrow channel through which all maritime traffic going to or from the Baltic Sea must travel - has been one of the most crowded and intensive shipping areas in the entire World over the 75-odd years since the end of WWII. And yet...... over all these years there's not been one single loss of (or serious damage to) a ship in the Skagerrak. Or anywhere else in the Baltic Sea.
"But how can that be?!!", I don't hear you ask. Well, since you don't ask, the reason is this: all of the shipping lanes, and everywhere remotely near those shipping lanes, was cleared of mines and other ordnance at a surface- or sub-surface level within a decade or so of 1945. Of all the UXMs etc that remain in the Baltic Sea to this day, they are all either a) way clear of the shipping lanes, or they're lying on or near the sea bed (thereby posing no risk at all to ships passing overhead at surface level).
There is effectively zero chance that the Estonia somehow hit a left-over mine (or similar) from WWII (or similar). Literally dozens of ships sailed that lane every single day, and had/have done so for the past 75 years. It's functionally
impossible that one or more mines (or similar) suddenly materialised close enough to the surface, and close enough to that shipping lane, as to pose a mortal risk to the Estonia - when this had/has never happened at any other time before or since.