Any examination of the efficacy of shield crackers without considering Marines is only looking at half of the story. Seltorian ships are built with significant numbers of transporters and entire colonies of Marines.
Use them.
     The whole "historical point" of the shield crackers was to be able to board and capture ships intact. (The Tholians were businessmen and wanted to get back stolen resources, not destroy them.) Seltorians have more Marines than anyone-else and plenty of transporters. Either perform hit-and-run raids (if you can't capture the ship), or perform boarding actions (if you think you can capture the ship).
     To capture an enemy ship during a duel, remember that you only need to have some of your Marines survive the first turn. The idea is to build up enough numbers so that by the third turn you outnumber the enemy ship's Marines and you will eventually capture the ship. Shield crackers help you do this.
     In a squadron scenario, you should be able to just flat-out capture enemy ships in one shot. A Seltorian task force of a light cruiser and a pair of destroyers (or frigates) will have 14 transporters (seven in Fleet Scale, against smaller targets), which will allow you to send over enough Marines to overwhelm most opposing cruisers, and at least challenge the Klingons and Gorns. Do it a second time and the ship is yours.