I noticed with S4 patch, the fx for Mask Energy Signature no longer darkens my ship. Is this intentional? I kind of liked having the darkened ship effect. And I know MES is not an extremely popular ability but I use it quite frequently in pvp matches as a poor man's cloak. It at least keeps the Klinks from targeting me first.
I use it for the same reason. It not only works well in the initial volley as a nice surprise to the opposing team (zooming around behind them and de-masking to fire a gravity well from behind while the rest of the group hits from the front/sides) it also gives you the ability to zoom into the edge of the later furball fight without being noticed until it's too late. Punch in an Aux battery before you use it and you can get pretty close to a ship not expecting you to be there. The drawback is that it takes up a valuable LT slot and you can't use it in combat, but it's certainly useful. For PvE missions, it also enables you to tag scan missions without being noticed in many missions. Computer ship sensors are usually much worse than player ships.
I noticed the reduced FX on the patch as well. It's almost not even noticeable but you do see a slight fade on the top sensor pod on my Nebula but that's about it. The only other visual indication is a badge noting MES on your ship effects and that's not really helpful. The darkened ship usually helped me visually note if i had the thing on or not, since the skill tab gives you no indication you have it activated.