If the accountant has to do a formal audit he/she has legal responsibilities, which should include satisfying him/herself that the accounts are an accurate reflection of the state of the business.
If sucha formal audit is not required then an independent investigation should be undertaken. However, how you persuade the owner of this I don't know!
Of course, it may all be above board & she just likes working in utter chaos, but if there is cash & cheques just left lying around it would be indicative to me that her accounts work is unlikely to be able to be all that accurate. You just can't do that sort of work thoroughly if you don't have some reasonable organisation.
If the business doesn't make a profit then either the selling price is too low or the costs are too high - or both. Unless of course your suppostion is right & there is something underhand going on. Perhaps you could use the lack of profit to try to persuade the owner that a proper investigation is needed.