To answer your questions
1. Yeah, you can use the flashcart at any time you want.
2. No, until now, no risk at all. 3DS won't get bricked because of using the flashcart, and you can just feel free to update your 3DS at any time. There is only one rule you should notice, update the flashcart before you update the 3ds console.
3. Always recommend three cards. r4i gold 3ds, acekard 2i and dstwo. if you want to play gba games and enjoy other powerful features such as real time save, real time menu, slow motion, dstwo is your only choose, it is the best but also most expensive. and if you only want to plat ds games. Then just choose the r4i gold 3ds (official site should be r4ids.cn) or acekard 2i, both of them are very goopd cards. By the way, another notice, 3ds firmware has been updated to V4.2.0-9 two days, acekard 2i can not work on it until it releases update patch later, so if the 3ds you receive is alreasy on the latest firmware, you can only choose r4i gold or dstwo. And i personally love R4i gold 3ds better,so i recommend this card more.
4. THis is site i recommend: Buy acekard 2i, r4i gold 3ds, dstwo, ace3ds flashcards for low prices-dsflashcart.com this site is also recommended in this forum here: http://www.wiihacks.com/recommended-...hcart-com.html By the way, now that you will trade your DS console for the 3DS, so you'd better buy a preflashed card, which means you dont need to update it by yourself when you receive it, the site i recommend will match this demand.
ANy other questions, feel free to leave the reply.