FASA Games, Inc.

So I was pondering taking a loan in a FS game and couldn't understand how silly the system works. You have to pay to deposit money with banking institutions. The reason this is silly, is that there is less incentive to do so than say if the payment took place during the withdrawal. As a bank, you want people to give you money so you can then in turn invest it or give loans out to others. By doing the opposite, it makes it so that organizations will be less likely to give regular deposits but rather wait until they have large sums to place in keeping. Further, they will have no qualms about removing money from the bank as there are no fees associated to withdrawals.

I think you need to look at the lenders in the Empire in the context of historic (pre-20th century) banking rather than the way financial institutions work in the electronic age.
Lenders (typically Reeves or Brother Battle) will want security for any loan - that might be a piece of property, anexisiting financial investment, proof of liquidity or some such and they will most definitely insist on a legal contract concerning the terms of repayment and interest.
They will be making their money on the interest (and potentially anything they are holding as security) and in the case of interstellar organisations (I.e a Guild or religious sect) they may not expect you to pay back the lender themselves - just another "branch" as it should all balance in the end.
However woe betide the individual who reneges on one of those contracts....Muster bailiffs or Brother Battle debt collectors are not to be triffled with....

I'm not arguing the loan system is out of whack, but the deposit/withdrawal system is. The deposit/withdrawal system is what supports the loans, yes. Thus your prerogative is for people to keep as much money in your financial institutions as possible.

A few years back (like 30) in order to have access a loan, you needed to show yourself as a "good payer". That way, you would get a credit (or more credit) according to how well you pay your loans.

Again, the Reeve benefits already by having the money in the bank. Further, it is to the Reeves' incentive for you to not withdraw your money so they have access to a large sum for longer.

In your example of the banking script, you have no benefit charging them at deposit than at withdrawal. In fact, if they are delayed or never make it to destination, the withdrawal will be delayed. The money is still accessible for them.

And major institutions, nobles and churches are more likely to be able to have their own physical treasuries to prevent theft. Further, it's more difficult to steal things like land than money so it's almost ideal for them to continually invest into infrastructure, real estate, or purchase assets if storing money away costs you money and you don't get anything in return other than some security.

Another book explains interest charges in the Known Worlds range from 20 to 50% (factors being if you are a member of the League, level of risk, etc).

Which I think motivates the Reeves to want to have more coin when their profit margins clearly lie on the loans side as opposed to the savings.