Well using some new tech i developed after uploading the database I had a look at your design, adding the new CIWS seems to have made it more heavy/slower but it is roughly along the same lines.
Ah I guess what doesn't help is the newer power plants are internally armoured
Emperor class Battlecruiser 31750 tons 3248 Crew 9599 BP TCS 635 TH 900 EM 0
5905 km/s Armour 20-89 Shields 0-0 Sensors 1/1/0/0 Damage Control Rating 67 PPV 188
Annual Failure Rate: 171% IFR: 2.4% Maint Capacity 8881 MSP Max Repair 620 MSP Est Time: 3.59 Years
Flag Bridge Magazine 1000
Naval Magnetic Confinement Fusion Drive (30) Power 125 Fuel Use 40% Signature 30 Armour 0 Exp 5%
Fuel Capacity 750,000 Litres Range 106.3 billion km (208 days at full power)
Quad Naval 25cm Soft X-ray Laser Turret (2x4) Range 360,000km TS: 12500 km/s Power 64-20 RM 6 ROF 20 16 16 16 16 16 16 13 12 10 9
CIWS Mk2 (1x10) Range 1000 km TS: 32000 km/s ROF 5 Base 50% To Hit
Beam Fire Control Mk3 (1) Max Range: 360,000 km TS: 10000 km/s 97 94 92 89 86 83 81 78 75 72
Standard Magnetic Confinement Fusion Reactor (4) Total Power Output 40 Armour 2 Exp 5%
Baracuda Missile Launcher Mk2 (10) Missile Size 10 Rate of Fire 60
Baracuda Mk2 Fire Control (1) Range 58.3m km Resolution 60
Baracuda Mk3 Anti-Ship Missile (100) Speed: 37,500 km/s End: 20m Range: 45m km WH: 16 Size: 10 TH: 525 / 315 / 157
Basic Active Search Sensor (1) GPS 8000 Range 48.0m km Resolution 100
ECCM-3 (2) ECM 30
Missile to hit chances are vs targets moving at 3000 km/s, 5000 km/s and 10,000 km/s