Built in desk
I made a built-in desk and shelves for my home office. Two months of work and more mistakes than I care to admit, but it turned out okay in the end...
construction - Building fitted desk for home office - Home Improvement Stack Exchange
Ambitious built in cabinet/desk plans
Sketchup online will do the job, it's an easy to use 3D modeling software and it's widely used in interior design and woodworking. The online version is free and should be enough for your project, the paid versions are overpriced.
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My husband and I built an office space for him in our main living area. We used 2 Billy Bookcases, 2 Sektion Base Cabinets and a Karlby walnut counter top. Whole project took about 3 days. We have a few little touch ups and some decorating to do but I’m really happy with the result! Before and after included.
To answer your questions in reverse order: 3) Install your floor coverings first. It will go faster and easier if you have no obstacles to work around. You can always cover the new floor with tarps if you need to paint, drywall, etc. in the future. 2) If you need to lower the height of the cabinets ,as you noted, the toe-kick can be sawed off so as to decrease the cabinets height by (+/-) 3 inches. If you need the height lowered further you will have to modify the cabinet carcass (think auto body chopping). 1) Laminate or wood? Completely discretionary. Whatever appeals to you. Laminate will take more abuse and more scratch resistant. Wood, on the other hand, is pure and elemental. Sealed with the right product wood will endure years before it needs to be re-sealed.
Note that nearly all kitchen systems typically also sell desk-height systems as many kitchens are now built with desk/work areas. So if you go the kitchen route, you may want to look into that option.
As for the work surface, sure, wood or laminate are both fine. And both used widely for this purpose. It really comes down to personal preference as to what you want.