It's not an "anomaly" it's a consequence of ship-specific strengths and weaknesses. If all ships were perfectly round metal spheres, then sure, all that should determine final shield strength is the installed shield generator and the mass. The actual shield strength depends on how efficiently the ship's shield generators can deliver the shield power. It's the same for thrusters, it isn't not just an issue of a certain size of thruster moving a perfectly round metal sphere where it's going to be directly proportional to mass. Some ships have particularly powerful/efficient thrusters for their size and this allows them to outperform other ships with similar thruster/mass ratios. The "hidden" shield factor is the same as the "hidden" thruster factor or the "hidden" thermal efficiency factor for each ship. Each ship has base stats that are then modified proportionally by the modules you install, but generally speaking certain ships are going have advantages due to their base stats. Some ships run particularly cool (Diamondback explorer), some might run hot (most Lakon ships like the T6), some ships have good thrusters (most Imperial ships) and other ships have good shield strength (Python and FDL).