The drawback of Quicken Home & Business is the same as its main benefit, namely that it combines your Home & Business together in an overall picture. For people bringing in limited income with limited expenses on the side, there probably is no harm in thinking of your business checking account as a place to get money to transfer to your personal checking account when there are bills to pay, and transferring money back to your business account from your personal account to pay bills. But, for someone bringing in a substantial amount of income, or as a sole source of income this can start to get dicey. And, if you have investors, or if you are taxed as a corporation, transferring money around like that is right out. (Which transfers count as pay, and which count as dividends or distributions?)
Another annoyance if not an overall con is the Deduction Finder. Most of the time, the deduction finder comes up with non-deductible things and asks to deduct them. On the other hand, it never seems to notice the things that are deductible. The problem lies in the fact that you should know which things are obviously deductible (the $40 at Dave's Business Supplies that you categorized as Supplies is recognizable as a deduction to blind socialist mice playing with knives.) For items with non-business sounding names and categories, the Deduction Finder will sit quietly by when you just might be missing a deduction after all.
Expect your accountant to sneer if you walk into his office with a data file from Quicken Home & Office. In fact, if you need an accountant to handle your business taxes, then you have outgrown this product.