About 1% of people get audited. The ones that do have audit flags. Being self employed is a small flag (a lot of people are self employed). People using the Home Office Deduction is definitely a Audit Flag (very few people have a legitimate home office) so its a flag (not a guarantee of an audit) however if your accountant tells you to take the deduction than take it.
The main reason I have been advised against it from 2 different Accountants is the Client or Customer Access section. This doesn't go into it to much but it touches on it. From what I understand its "strongly" encouraged to have separate entrances and parking for customers as well as signage.
The point I am trying to make is this, Your likelihood of being audited goes up just by being self employed ( but still unlikely) the use of the"Home Office Deduction" just puts you into higher risk class "less legitimate in the IRS eyes" and hence the higher potential for audit.
So to me its just not worth risking an audit when I can be aggressive with other areas of my return (mileage, travel, supplies, postage,cell phone,etc..) that are not scrutinized nearly as much.
Here is a small snippet from IRS.gov
One of my very rich friends told me the same shit. Basically the more you try to deduct and get away with the higher a chance you will get audited. He said it's better to just bite the bullet and pay the shit and don't try to cut stupid corners like deducting your home office. And since he has the best Jewish accountants money can buy, and he himself is a Jew, I listen to the advice he gives on the issue. So far...so good.