Yes on both counts. I started drawing an irregular shaped lake and it just didn't look right. Too much work for too little benefit making it look good. Also, water in OpenTTD has regular edges (on the isometric grid), it's got to fit the world style.
I would like to draw that bucket dredging machine.
Apart from the mockups presented in this threat it´s rather difficult to tell about the actual size of the FIRS industries. But judging from the FIRS building/HEQS vehicle and HEQS vehicle/other building, train etc.-ratio I feel they could be a little bit bigger (some 5-10%)....[...snip...]maybe the buildings could extend just to the edges
Some industries will have very large overall footprints due to repeating multiple buildings. We took a decision early on not to run buildings to the very edge of the tile, it's not original TTD style, and doesn't look so good (it's been done with some grf sets, so we did a few tests).
Take the brewery as an example[...snip...]unless you switch to transparent mode, you will have a hard time finding it in a somewhat bigger town.
Agreed, I'll think about this as a problem.
I don´t get why there is a gap between the main building and the boilerhouse
It can be built with a road or rail line (or canal) running through it. It also helps clearly show the individual modules that make up the industry (these can be rearranged to make different layouts).
Talking about the size I think about all the lorrys or traincars filled with the monthly production of this brewery and ask myself: where do they store it?
Fair point, but it's scaled and based on a real brewery. If we want to look at real life, they probably solved the problem by not storing much beer - delivering it often. If we want to look at game world, well how do all those vehicles fit in a single tile depot?

Meanwhile, if you want more storage, add warehouses as station tiles (using ISR). I'm deliberately trying not to replicate things that are provided by ISR. Industries will mostly feature tiles for raw material storage, but not much for finished goods, as the ISR station set can do that.
So, as said before, please don´t get me wrong, but for a serious high production industry some of the graphics don´t look so convincing in that particular aspect.
Most of them can have the buildings repeated to make a larger industry - layouts at random. We *may* relate the size of the industry to its maximum production limit (no promises). One constraint is that we have to actually fit the industries on the map (around other objects, and limited by underlying hills etc.)
cheers,
Andy