was under the impression that all scupper holes have a built-in Bernoulli effect of their own, hence one reason they are found on kayaks. While in motion, the Bernoulli vacuum pulls water from the cockpit.
Usually, but not automatically. For instance, the daggerboard well, CB well and drivewell all scoop water in. Scuppers having a teardrop recess behind them generally have a positive Bernoulli effect.
So why tape the scuppers? If a larger wing area creates more lift, would not a larger scupper (and more speed) draw water more efficiently?
Tape over the front part of the opening gives a huge boost to the venturi (when going forward). This is nothing new. You may remember the old vent wings on automobiles (that could also reverse and become ram ducts), venturi vents on the roofs of RVs, sunroofs and vent visors on cars. This isn't really about lift.
Or are we talking a "venturi" effect here, where narrowing an opening creates an acceleration of air/fluid which is already under pressure?
No, the boost comes from aligning the exit flow with the slipstream cleanly rather than dumping it. This also reduces drag. Keep in mind, if the boat goes backwards the venturi "vacuum" becomes a ram and the seat area will flood.
To demonstrate this powerful effect, hold a limp piece of letter sized paper with both hands up to your mouth, blow over the top of it (creating a lower pressure slipstream) and watch it lift the paper!