Walt
I admit my testing was not extensive, I saw 2 Crucible victories and stopped at that. For whatever reason, they were such crushing victories, I felt doing it more served no purpose, perhaps I should have.
I would probably agree built-in ships generally don't carry enough PD. But I prefer to build more interesting ships rather than stack missiles for days onto a pile of engines, so I typically limit myself to 2-6 missile launchers on any ship, even my biggest 2m+ designs. In my case, I don't really notice a lack of enemy PD because I'm not all in on missile only designs.
As for balance changes radically out-dating old ships well... I don't think that problem will ever go away. I mean adding new weapons and systems the old ships never had access to is going to create the same problem every time you add something new.
The way I've experienced this situation, there are two solutions. Upkeep your designs every time major balance changes are made, be it adding new weapons and equipment, or major buffs/nerfing to existing weapons. Personally I don't like that solution. Too much constantly having to go back and redo work you've already done.
I think it's perfectly acceptable to leave current designs as they are, but just create new designs when radical new systems require it.
Heck you can even have retrofits. Take a ship design, and rather than have its update replace the ship entirely, make a Mark II version. Leave the old ship as is, flaws and all. And apply whatever changes the missile balance requires to the Mark II. And in future if/when entirely new weapon systems are implemented, assuming you really like this ship design for whatever reason, make a Mark III.
There's nothing inherently wrong with sub-optimal or out-dated ships in a PVE setting, in fact they are a boon. A player will look at them and go 'wow what a junker I'll never buy that' but... so what. They aren't there for the player to purchase and win the game with, they are there for the player to fight against and to get blown up in spectacular fashion.
With stronger campaign elements, you can further use outdated ship models. For example, let's say you are undertaking several missions to attack/harrass some enemy empire or whatever. At first, you fight a lot of their old, outdated, poorly crewed vessels. Eventually, the missions get harder, and they start sending better more modern ships to fight against you. So with a proper faction set up, you may create sub-divisions of ships within that faction. Rather than randomly pick any ship from the entire faction's roster, there is an 'old' and a 'new' pool of ships.
Bottom line, PVE benefits immensely from a massive wealth in enemy variety. If every enemy you fight is a top tier design, with internal armor protecting well spaced out reactors and optimal weapon placement and perfect PD coverage, that will get real old real fast. Only the best, most important, and rarest of enemies should have that degree of design. It's a good player experience to fight through hordes of lessers to reach those really important enemy ships, and adds a lot of variety to gameplay.
Like I'm enjoying the fleets in Bounty Hunter mode immensely of late. It's a huge change of pace from 1 on 1 battles, and I think my ship designs have become far more interesting as a result, as opposed to just making bigger and stronger wall ships.
https://forum.cosmoteer.net/d/4717-a-new-ship-for-a-new-patch-designing-vds-guardian
TLDR:
So to you saying new PD changes might further outdate and unbalance old PVE ships, I say that is not actually a problem at all. It is an opportunity in disguise. An opportunity to have classes and subdivisions of ships based on the age of their designs, which in turn can be implemented to created stronger and more interesting singleplayer progression and campaign playthroughs. Old, sub-optimal enemy ships for early game opponents, new, better designed adversaries to fight later on.
Example: I consider the Wolf a bad design. Its reactors are too close to each other, and not protected by any shields and only very limited armor. But it's still a good ship, I like the Wolf. It's got overwhelming firepower that a small, shield reliant ship will struggle against (cannons with multiple EBs), and it's a lot of fun to blow up. Perhaps Wolf MK II can be a retrofitted upgrade, created as a result of new balance changes and equipment.
Better example: Diagon Death Dealer. No PD at all, and same clustering problem with reactors. But I think the Diagon is a really cool ship, it inspired me to try and make some diagonal ship shapes. I've yet to make a really successful one, but I luv the principle behind it. Diagon is a great enemy PVE ship that's not horribly threatening, extremely vulnerable to missiles, a lot of fun to destroy. The perfect ship to give an uncaring AI. Perhaps later in the campaign, DDD can be phased out for DDD MK II. So DDD MK II, when attached to an enemy fleet, is an upgrade over the early DDD players have fought and beat. That sense of enemy progression, not just in enemy ship size, but in enemy ship design, can give the player a sense of continuity with their gameplay.