This is intentional, and I agree such improvements should have a warning in the tooltip of said improvement.

I realize that this is intentional for many of the buildings, e. g. Galaxy Wonders and Capitals. I'd also understand if upgrades to special resources* were indestructible, but they are not. I do not understand the reasoning for planet-unique buildings in general: most of them are destructible. Why not all? (Or all indestructible to be consistent? Then at least you'd know what to expect.)

Anyway, whatever the reason, I don't need to be able to cook to enjoy a meal. But I'm not enjoying the meal served to Synthetic races: they only have a choice of two indestructible buildings at the start of the game. Ok, and the ship yard - but why do we even have to explicitely build a ship yard anyway??** There's no sense at all not to rush build it and start building ships on turn 1!

Even if the odd choice of adjacency and leveling types (of the Yor Extractor and Mainframe) were fixed to the point that they remain relevant to a race who can and will raise their pop to extreme levels, every advanced player knows that the tiles a planet starts with are often not the best ones to put central improvements on!

* P.S.

Just an aside: I've noticed that when there are tiles for 'mining' special resources, these are called 'trade resources'. Why?The AI are not offering remotely enough (and I'm talking of those where I'am supposed to have a diplomatic advantage), but at the same time they charge through the nose when they have to offer some of their own. That's not my understanding of 'trade'!

**P.P.S.:

What I meant is: why doesn't everyone get to start with a shipyard already there like how it was in the original base game, before Crusade? (and besides: how were the initial ships built without a ship yard?)

First let's why they made some wonders indestructable, and not others.

It started with the Brindles Observatory. This wonder gives you a free planet, and that was it. Gamers complained that all you had to do was destroy the wonder after you built it. I had no problem with this, even though this is a little cheesy. To fix this they made all wonders indestructable. Then several players complained similar to this that some buildings actually need moving later. The attempted balancing fort this is to make the buildings that don't do things after you initially build them that are galactic achievements indestructable. If they messed this up go ahead and report this.

The reasoning Brad gave for you to require building a shipyard if you wanted one was to give different ways you could start your game.

I almost always (but not every single time) rush the shipyard.  So what?  Let us all complain about something that really means nothing after turn one, ok?

I was referring to free constructors upon game start...

I never rush-build a shipyard(i also dont use constructors for it),

with the settings i play with it would be just a wast of money

If you want to start with a shipyard but not ships, take the constructor options and build a shipyard turn one. Boom, problem solved.

And no, it doesn't solve the problem, if you chose to name it so: the issue I've reported is that the synthetic planetary hubs are indestructible. I've explained why that is a problem (useless later in the game, no choice of long-term-useful improvements to build at game start), and in a P.P.S. I've mentioned just another weird issue (the removal of ship yards) that I've noticed in this context.

Please note that with respect to ship yards, it's not that they're missing - I know how to build one. It is the lack of explanation or even remotely sensible reason why they were removed in the first place. Also note that it doesn't matter whether you choose to use a constructor, build it normally, or rush it. My point is that no one will complete a game without a ship yard at their home world.

The only answer I received on this topic is that it was done "to give the player more choice". But in fact, removing the ship yard is forcing a 'choice' on the player, because it makes no sense at all not to have a ship yard! If it were added back in, that would give the player more choice, because then he could decide to build whatever ship he likes on turn one, and on top of that (rush-)build something useful on the home world!

And I've neglected to mention that you get your admin points refunded when you build a shipyard with a constructor.

I doubled checked myself at it appears to be the case even with the starting constructor, which is only fair given its deducted from your starting admin cap.

Personally I prefer the 3 scout start...lets just say they were assembled on the planet and call it a day.

That is correct.