The cup seals take up significantly less room, which is important for smaller boats. They're likely less prone to damage from pointy tools during maintenance as well. Bellows (rubber boot) seals apply force on the servo when retracted or extended as the rubber fights to return to is formed shape. The cup seals may require more force to move (marginally), but they exert no centering force on the servo once in position. Bellows seals are more forgiving in regards to alignment. Typically servo throws change the angle of the linkage slightly, which can result in binding in the tight tolerances of the brass housings of the cup seals. Cup seals do not seal pressure well when it goes from the inside out. They work best for pressure going into the WTC, not out. They're basically uni-directional, so not good for pressure style systems like piston or pump that pressurize the dry areas.
I, personally, use bellows seals simply because they're simple, easy to find, cheap, and easy to mount. Both work, pick your poison.