Thoreau says that farmers claim bankruptcy only when they actually have no money. Merchants, on the other hand, claim bankruptcy when it would be merely inconvenient, not impossible, for them to meet their obligations. That is to say, merchants actually have the money they owe their creditors. They just don't want to part with it, because doing so would be inconvenient.
The whole point of setting up a limited liability company, for example, is to insulate a merchant from any losses or bankruptcies or financial judgments against the company. Let's say I set up an LLC and get 5 million dollars in investments. Six years later, I realize that the company isn't doing as well as I and my investors had hoped. In fact, its debts and liabilities far exceed any assets and profits. It owes 1.8 million and is forecast to keep losing money, while its assets amount to maybe $250,000. And there is no foreseeable way the company can repay what it owes investors and/or creditors. I therefore declare my company bankrupt. As far as the law goes, this is quite legal.
But let's say that during the six years of the company's existence prior to declaring bankruptcy, I have paid myself $500,000 per year as a salary from the company. Again, this is quite legal. What it means, though, is that I personally have earned $3 million, while my company has lost $1.8 million over the same period. The company's shortfall could probably be covered from my personal funds. I might need to sell my house and other companies, close my bank accounts, convert my other assets into liquid, etc., but I could probably raise the money. However, that would be inconvenient: I would lose much, if not all, my personal wealth. So I just let the company fold, leaving my investors and creditors to absorb the losses. All quite legally.
Or to take a current, real-life case: Johnson & Johnson, facing lawsuits for using talc in baby powder despite its being a known carcinogen, spun off its talcum power unit into its own subsidiary so that all the liabilities of the lawsuits would be held by that company. The billions of dollars of assets of the parent J&J company would thereby be protected, while the subsidiary could declare bankruptcy. So J&J wouldn't have to pay out any of the lawsuit judgments/settlements at all. The legality of this breathtakingly cynical manœuver is still undecided. A US District Court said J&J couldn't do that, but J&J is appealing to the US Supreme Court.
Thoreau says that a farmer unable to pay debts (say, because the crop has withered for several years due to drought) has failed honestly, and is bankrupt merely financially. But merchants who forgo paying their company's debts despite having personally enriched themselves though that company are "bankrupt in a worse sense than they who fail honestly": they are morally bankrupt.
A certain former US president who bankrupted several of his own companies also comes to mind.
(I'm aware that the legal and financial workings of LLCs are more complicated than in the oversimplified example given above; it's meant merely to illustrate the kind of thing Thoreau means. It's also true that "farmers" in the US nowadays are likely to be agribusinesses of the same ilk as J&J rather than the salt-of-the-earth types Thoreau envisions.)