The rules on morale aren't completely clear and I've run into problems with them. It's quite possible, especially with a large ship that has 20-30 components, and a couple dozen endeavors under their belt, to have ships with a morale of 150+, which is quite absurd. Archeotech components should count as BC, as implied under the sidebar Craftsmanship and Morale in Battlefleet Koronus on page 17. The same sidesbar states that such components cannot increase morale "to above the ship's maximum level," while never stating what contitutes a ship's maximum level. The core rules specifically state (p. 224) that morale lies in the range of 1-100, not 1-100+. Then again, there's at least one supplement out there with rival RT ships having crews with morale in excess of 100. All of this = confusion. The problem comes when looking at the average Imperial Navy ship. Should RT vessels be regularly sailing around with morales higher than a naval military vessel? There's plenty of historical evidence to back up either argument if you want to use the Age of Sail as evidence.
Here's how I've handled it. Components and upgrades that specifically call for a morale increase/decrease raise/lower the "permanent bar." Quality can only be used to offset decreases, but not increase morale above the "permanent bar." For example, after adding all stated increases (Temple-Shrine, etc.) and subtracting all stated decreases (luxury passenger quarters, etc.), you have the "permanent bar." Good quality can't increase morale past that and poor quality can't decrease morale past 1/2 that. This sets a reasonable upper limit so my players never again have those ships with 150 morale and encourages the use of some components that might not otherwise ever see the light of day. This means the absolute upper limit of morale is about 114 (not including a Euphoric Life Sustainer which could increase it to 122 at the cost of 10 Crew Rating). I find that more reasonable. As a side note, since putting this limit on morale I've seen a giant increase in the use of Bilge-rat Quarters.