Let's just differentiate here between 'UNTIDY' and 'FILTHY'. Common and professional courtesy dictates that the pilots should tidy up after themselves. Removal of flight deck gash bags and disposal of used water bottles and newspapers as well as wrappers and other garbage should be done by the pilots. Usually placing these items into one gashbaag for the cleaners to remove is sufficient. Stowing manuals and charts or leaving them tidy for the next crew should also be SOP for anyone employed on the flight deck.
As far as hygene, that is a separate matter. I remember joining my first jet airline and being given a 2" paintbrush and told that I can either use it to paint my home during the quiet winter months (whatever happened to those?) or else use it to clear away the accumulated dust (mostly dead skin cells) that gathers in every nook and cranny on a flight deck. Unfortunately, I noticed that every time I used it to 'dust', all I seemed to be doing was rearranging the dirt as it would just fly up into the air and swirl about before settling back on the screens and into all the other orifices!
As to other dirt such as crumbs, wayward peas, coughed up boiled sweets, half chewed food and everything else that gets spilled or splashed around the flight deck (and that's just from me!) it really begs the question, why isn't something done about it? Some companies arrange for a 'deep clean' of the flight deck when it goes in for heavy maintenance but judging from the reality I have seen in the past, that is little more than the 'rearranging' of the dirt and dust that I mentioned earlier.
Perhaps it's time that someone, perhaps our professional associations, should look into the hygene and health safety of the flight deck. Maybe I should start a company that specialises in deep cleaning flight decks and offer the services to the various airlines. Something along the lines of a crew of cleaners who are trained in dealing with flight decks and aware of the need to be extra careful about pushing switches etc.
Even if cleaners are allowed onto the flight deck to vacuum the dust, why shouldn't they be allowed to wipe down the panels and sills? The next crew should still do their pre-flight scans and put right anything that has accidentally been left out of position.
Let's be specific here when we discuss the state of our flight decks (offices). We are talking about cleanliness and hygene. How many companies would invest umpteen millions of pounds/dollars in their offices and then fail to have the cleaners look after the state of their management offices? None probably except airlines of course. Contaminated air may be one problem on some aircraft types but I'm fairly sure that unhygenic conditions on most flight decks probably leads to more lost days work to various sickness overall.
Hmm... I feel a poll coming on.