BTC market (what technology and aproaches)?

I am not an IT guy so please bear with me. I would like to bring some idea into discussion with our IT guys later this mont.

We are developing a new market for virtual currencies. Something like vircurex or btc-e.

First question: - technology
Our plan is to trade BTC, LTC, NMC , PPC etc so I am thinking about using bitcoin-qt and altcoin-qt clients and use its API functions. I thing this might be the fastest from the programing point of view as they all are just clones of Bitcoin. However I do not know if there are any alternatives.
I was also thinking about using Bits of proof (BOP) API, but they are focused on Bitcoins only. Electrum is very fast on implementation, but do not think it is reliable for high volume of transactions and we do not want to use block chain API too as we do not want to be dependent on 3rd party services.

Second one: security
I am aware, that we will need to keep virtual currencies in the Cold wallet and keep min. amount of currencies in HOT wallet for operational purposes. I am thinking about 2 different approaches but do not know which is better:
- to store all customers receiving BTC addresses in the cold wallet (watching dog wallet). I would like to use some API calls to retrieve information about received funds etc (do not know if bitcoin-qt is good for such operations). We will need to transfer funds from the cold wallet to hot wallet manually in order to process payouts automatically. Is this good idea or is better to keep all customers receiving addresses in hot wallet and automatically move funds to cold wallet? .

Last question - wallet approach:
Lets say, there are 100 accounts in our market system. Each account can create basically unlimited receiving BTC addresses. Would you need to create 100 differrent wallet.dat files?
Or is it better to have 1 wallet.dat file containing all addresses of your customers? I like this idea more, but do not know how to handle change payments?
What your take on this is and what would you guys recommend us. What is the best business practice?

Thank you.
Daniel