AS many have said a linkshell/guild bank is a very good things and honestly it causes no problems only helps the guild advance... the issue comes into play with leaders who have no idea how to keep records for the bank or just plain out corrupt leaders who steal from it.

My ls currently has a bank in XIV and it had it in XI. We actually have a whole custom built accounting system to keep track of who has what, how much of it they have, and what each member is able to withdraw from it. It provides a trade system for member to easily get crafting materials, allow for members to withdraw item from the bank for dkp, provides a central unit to sell excess gear drops and will provide food, meds, expensive ammo, and other event related cost.

If you want a bank to work it is simple:
1) Never let 1 person hold everything... this is really bad. Theft is always a risk, and 1 person holding everything yea...
2) Keep Records of everything... every single transaction must be recorded as soon as it takes place. Member must know how the bank is spending and making money, and it must be visible.
3) Only allow people you know to hold bank... if it is a new shell do not start a bank at the start. My leaders in Paradox have been with me for over 2-3 yrs, so I know them and the chances of them bailing with bank are a fraction of what a newer member would be.
4) Person who handles the balancing of the books and what not, Does not hold gil/items. Simple accounting policy the one who keeps records does not hold money/assets.

The issue with everything above is the paperwork, and the more the bank does the worse the paperwork/transaction time becomes. That is where linkshell's get lazy for the most part and a crooked person will use that time to skim funds or outright make false entrees and it will fly under the radar. A simple bank to truly keep good records will probally be around 2-4hrs a week of paper work, my bank system was about 10-15hrs/week until we made the automated system, now it is back down to 4-5ish hrs.