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How unhygienic are cut flowers from a garden - what sort of mould, fungi, etc. are on them? I was wondering if there was a source of this sort of information somewhere online.

have you tried an internet 'search'?

If you are that concerned, my advice is to leave them in the garden. The cut flower industry is worth billions worldwide, cut flowers are sold everywhere from petrol stations to shops in hospitals, if the threat from cut flowers were of serious concern, they would not allow them into hospitals (some do ban them but only on the ground they are messy), most cut flowers now have a sachet containing a mild bleach to stop the water from going green and smelly, but that is only for convenience rather than health matters. Moulds and pollens are all around us, in our homes and gardens, you cannot keep yourself apart from them unless you seal yourself into a bubble

^Mouldy