Problem with pint sized countries is that they can not bail themselves out in case of trouble because usually the banking sector is many times their GNP eg 24 times in case of Luxembourg. Look at Cyprus now like Argentina they are considered a pariah nation in financial circles.
It does not have to be a Maltese bank i.e. what happened in Cyprus is that your account was affected even if it was with Barclays, in Cyprus and that's what will happen in Malta if they get in trouble...
So if I have a Maltese registered fund, you claim my bank account in WestPac in Australia (just to make an example), they will tax the deposit (bail in)?
Yes, but my logic is: different jurisdictions for all that can be diversified. Never all eggs in one basket
Here is a guide on how to set up in Malta. http://www.hedgeweek.com/special/hedgeweek-guide-setting-alternative-investment-funds-2010