I think since they refuse to show evidence they have enough funds, it should be assumed it's a scam until proven otherwise. Really, they're making tons of money off fees, they are the most expensive exchange. Screwing customers like that is below acceptable. They're not just some paid app that can go down and customer won't be affected too much. It's money. Lot's of them. You can't refuse to pay and keep silence, otherwise you're a scammer.
It's a good rule of thumb to assume incompetence instead of malice. In the instance of MtGox it just doesn't make sense for it to be a scam.
They ran a business for a few years in obscurity then when they become a central figure in potentially a massive change in financial infrastructure they decide to run off with the silver? MtGox had the potential to be worth many billions if they were a significant service provider in a successful BitCoin scenario. They possibly still do to some extent if they can get their act together.
The assumption isn't that they ran off with the btc. It's that someone else did, now they are insolvent, and to prevent the fallout they are trying to live off the float and hide their insolvency until they have made themselves whole again.
I personally would never give them my business ever. Many people won't either. I'm sorry, they already screwed me once last year holding withdrawal for 2 days, now again. They are going down in history. The only question, again, if they will return the coins. I doubt they will. Even if we assume incompetence, it doesn't mean they suddenly can't SPEAK, right? Go and tell your customers what's going on. When people are not open about things, it most likely means they want to screw you and you are safe to assume this to be the default version.
Even in the absence of overt theft on their part, if the real explanation is not what they are offering, then it is still very likely a scam. That is, they are not disclosing information to customers that would be relevant to the customer's decision to use their service.
So, for instance, with the fiat withdrawal problem, if the actual issue is that they are not solvent, but are hiding this fact in order to become so through trading fees (a popular theory), then they are shifting an extraordinary amount of risk on to the customer without his/her consent. That would represent willful misleading for their own gain.