If the purpose of the stones is to break up the power of Storm Surges, which could undermine the Sea Wall, then it could quite easily have been accomplished by putting in a Rhos style Rock Groin further out in the Bay.
Why not do what they do down in Cardiff Bay and build a barrage which could double up as a berthing facility for larger cruise ships?
Cost.
If the purpose of the stones is to break up the power of Storm Surges
Actually, you're conflating two rather different concepts. The purpose of the stones (as I've said) is to dissipate the energy of the waves. Those waves are often (but not always) caused by a storm. A storm surge, however, is the dome of water that rises beneath an area of extremely low pressure centre and which is being pushed by near-hurricane strength winds towards land, resulting in an exceptionally high tide. Very little can withstand those, especially if they occur on or very close to a Spring tide.
In the UK, we also have some of the highest tidal ranges in the world. The top seven are in Nova Scotia, while we come in at number 8, which gives some indication of just how extreme our normal tides can be. Spring tides (not to be confused with a season) can occur every couple of weeks, when a syzygy between Earth , Moon and Sun occurs. However, these monthly cycles are not the extremes, as the proximity of the Moon to Earth is also an important factor. At perigee (closest) we experience what most refer to as 'Spring tides' which can be significantly greater than usual.
What it comes down to is that we
can engineer our way out of it through groynes, or berthing facilities or a hydroelectric scheme, but only providing both the political will exists and the money can be found.