If you do not input your password in the Hotmail account when you create it, it should ask you for the password each time you start Mail (though it may not if Mail is running int the background, I'm not sure).
You can, of course, delete the account when not in use (or just turn off the mail syncing). You do this in the Settings app under Mail, Contacts, Calendars, and select the account.
Other than passcode protecting the entire iPad, that is all you can do for email security in the Mail app.
If you set your Hotmail account up as an Exchange account it will sync your server side folders (not local folders on a computer).
Setup Hotmail as Exchange
How To Setup Hotmail Using Exchange ActiveSync On Your iPhone, iPad And iPod Touch For Push Email, Calendar & Contacts – iPhone Hacks
To see folders in Mail, select the Mailbox button at the top of the mail list. You should see two lists. The top list is just Inboxes. There may be an All Inbox choice if you have more than one account. The bottom list is accounts. If you select this you will see all the folders for that account, including the Inbox.