grampybear,
The simple solution to reducing the complexity of too many "unwanted" goods is to disconnect delivery chains by using two or more stations that are not linked at final destinations like Book Stores or Shopping Malls, etc.
Here's an example from recent versions of pak128.open from the nightly build page.
Let's say you have A, a set of farms (sheep farm/cotton plantation) that supply a nearby Textile Factory, B. B sends it's textiles to C, a shopping mall. In pak128.open, the cotton, the wool, and the textiles are all of cargo type "piece goods". You set up a transportation network for this and everything's fine (ie simple).
But then you notice that the Shopping Mall will happily receive even more textiles than you have been able to ship, so you locate another textile factory D, which is supplied by nearby farms E. So you set up a second network E -> D -> C. But to save money, you deliver these new textiles to the same station at the Shopping Mall.
You think of this as two separate chains of textiles delivered to the same end destination. But the game sees this as one complex network of bidirectional connections. If A -> B -> C, and E-> D -> C, then because the connections are two way, C-> B -> A, and C-> D -> E. In particular though, the farms at A are connected to the textile factory at D, as are the farms at E connected to the textile factory at B. So if any of the farms in A happen to have D (as well as B) in their list of consumers in the factory window (when you click on the factory), they will happily start shipping to D as well as B. The route is A -> B -> C -> D. Similarly you may have E-> D -> C -> B. So you may end up with lots of raw materials gathering at the Shopping Mall, C, waiting to be picked up by the vehicles that deliver textiles to the Mall. (Important note: this is only because the raw materials are the same cargo type, piece-goods, as the finished textiles.)
But if instead of sharing the station at the Shopping Mall, the second textile chain uses it's own disconnected station (disconnected from the other station, not the mall!), then there is no
transportation connection between the factories at B and D, so the "complexity" doesn't occur.
A central warehouse will help to manage complexity, but it won't reduce it -- in fact it is likely to increase it by revealing more connections between industries which happen to be linked in their supplier/consumer lists and use the warehouse at some point in their transportation chains.
On the other hand, one can always embrace the complexity as a challenge, which is what I've recently come to do after years of cursing it. It's one of the things that makes SimuTrans a very deep game and replayable for many years.
Anyway, hope this helps.

PS. When I say that two industries are connected by a transport network, I don't exactly mean that are simply connected by, say, rail and trains. The other requirement for connection is the particular cargo type be present in every stage along the way, in this example, piece goods.