1. Can I use a SSD for the install part of Amahi? I'm a little confused on the install, you have to use a USB drive?
You can, but will be of little benefit. The officially supported method of install for Amahi is CD/DVD. See
http://docs.amahi.org
2. Can you manually update apps that are outdated in the store? Common theme I see with certain NAS "stores" the apps don't always show updated on website. I have no linux experience so not sure

Yes, but not recommended. If you break something, we do not support it. Our LIVE apps are mostly current. Occasionally we are behind on updates, but typically only one version and for a short time.
3. Any known problems with sickbeard/SABnzbd/crashplan that I should be aware of? My system will be plenty powerful for it, just on the software side i'm wondering.
Not really.
4. can you use apps that are not listed in the store on system as long as it works with linux?
Yes, but if you need help with install or break Amahi, support is extremely limited. Mostly only from other users in the community.
Why don't you offer a single install OS and not have to use web based? I would gladly pay extra for that feature. Lots of people feel very wary of signing up for anything now-a-days.

It may be harmless sure, but it certainly is not required or needed.
In order to link all the pieces, having an account and using the website is required. The install method is rather simple and painless for most. A single CD/DVD is all that is required.
Also please understand this is an Open Source project, mostly free and maintained by an all volunteer team. We do our best to keep things moving forward.