1) Either the Lucifer's Shivans are different from the Sathanis' ones (what exactly this difference is is anyone guess), and so they don't share the exact same technology (and maybe don't have the same goals, but that's another problem).
I doubt that. Shivans are Shivans. It was a scouting force. Sounds like over analyzing since FS never hinted at them being separate branches of Shivans. I also recall the FS2 game box saying that it was a scouting force in the Great War.
2) Or the Lucifer was a very costly prototype, and its destruction made the Shivans abandon the project (that's probably the same reason why we didn't built another Hades after the GTI rebellion).
Cost, economy, money, is all a human concept because humans don't think like a hive. Money is only there in society to create a chain reaction of cooperation and only represents a resource or service and also represents the cooperation of society and getting something in return for providing work for society. The Shivans don't care about doing something for something in return like humans do, and cooperation isn't an issue since it is all for the good of the race and they are a hive making rebellion also impossible among themselves, which would be the main reasons why they are superior, I guess. Plus, they seem to have no problem with resources in which money would represent and therefore have value. Meanwhile, you have Terrans destroying each others' resources because of rebellion which is their weakness and makes them overall weaker because of their individual train of thought.
If the Shivans did have a lack of resources, they would get it from planets, but they don't care about planets. That indicates no shortage with resources.
3) Or the Lucifer wasn't the only of its kind, but after the destruction of FS1's Lucifer, Shivans decommissioned the other Lucifers (high maintenance cost ? obsolete technology ?)
It was probably the only one of its kind, but maybe not. I do highly doubt that any of the Shivan ship classes are new though. They've been around for many thousands of years, no doubt in my mind. The ancients also said that the destroyers darkened their skies like a plague even way back then, which tells me they must have encountered more than just the Lucifer fleet, maybe sathani too. The scouting force itself may be obsolete though compared to some of the other ships in FS2 since it lacks a lot of weaponry, but that was probably only for balancing purposes. They just brought in different ships in FS2, like the superior Nahema because they are taking the GTVA seriously, not new designs, since a race that old should have all that stuff already and still have better ships that weren't in FS2 waiting somewhere. The ship classes in FS2 could be newer, but all of them must be 1000's of years old, no doubt.
Why would one think that any ship that the Shivans have is anything new when they have been a space faring race for who knows how long? Surely their newer ships would be even better than what we encountered and they may have already reached the technological limit; we just haven't seen their even newer ships and their true power. They probably have Dyson spheres too in their territory.
4) Or Shivans still use Lucifers, but none was encountered during the Capella incident.
Maybe, but I feel that the Lucifer was only there to lead the scouting force. Perhaps only one Lucifer in existance, and if others do exist, they lead other scouting forces like the one in FS1. But there is no need for more than one scouting force since Shivans probably go 1000's of years before having to eliminate another species. Seems that they are the only ones left in that part of the galaxy besides Terrans and Vasudans. Who knows how many races they killed and it would explain why the galaxy seems to only have them as a space faring race (or super race force of nature) and the Terrans/Vasudans being the only other space faring races in this galaxy.