Very little of what is actually needed to reproduce an experiment goes into academic papers. What you'd really want is a more formal, digital version of the "lab book". Experimentalists are taught, from their earliest days as an undergrad, to keep notes on what they're doing. The idea is to put everything useful in there. Got a new piece of gear with a long startup procedure? Put it in your book. Designing an experiment? Put the design in there. Ordered parts? Make a note of it. Running an experiment and finally found a way to do things that works? Write down the procedure. Got some results from your experiment? Print them out and paste them in your book. Saw something odd? Write it down. The result is a linear log that tracks a lot of stuff, both useful and useless. With experience, you learn to make use of tables of contents and margin notes, but searching through them for something dimly recollected can sometimes be time consuming. Lab books are where the gory details of how to actually do things is stored. The procedures, diagrams, and details in them are simply not conveyed in papers because there's no space for them, and many are viewed to be "common knowledge", although this kind of knowledge is probably only common to a small number of labs in the world.

The problem with these lab books is that they're often the personal property of the scientists and, as such, almost a sort of diary. They're written with yourself as the intended audience and can sometimes be impenetrable for anyone else. If you're working in a commercial lab, as opposed to research in academia, these books might be considered the property of your employer. In this situation you might try to make them more friendly to other human beings, but that often isn't a priority.

Putting things into a digital form would, in general, take a lot longer. Even with good proficiency in LaTeX, complex equations are quicker to just write on paper. Hand-drawn diagrams are also very common in lab books, and the software/hardware to draw easily in a digital form is not yet ubiquitous. Finally, digital storage occasionally dies. A lab book is a precious possession whose loss can cause months or years of difficulty. Physical hard-copy is easier to store long-term. Some people have undergraduate lab books from half a century ago sitting on their office bookshelves.

There is nothing that is technologically insurmountable to moving to a digital lab book format. Microsoft's surface tablets make digital drawing pretty painless. Cloud storage could be maintained long-term. Etc. The benefits of digital lab books could be considerable. They'd be easier to search and distribute. You could include copies in a digital appendix to an experiment (currently, most journals discourage large attachments because they don't like to pay for storage). To my knowledge, nobody has actually put everything that's needed together into a single cohesive program. You'd want a note-taking program with full LaTeX and freehand drawing support. You'd need to be able to paste in tables, graphs, and data files easily. It would need to have a long-term archiving solution and a really good interface. It would need to be as fast or faster than writing on paper for pretty much everything. It would also probably need to be open source, as scientists would probably not trust proprietary software that might make their notes difficult to access at some point in the future. Finally, the hardware to run it on would need to be ubiquitous.