The fact is that browsers can't talk to (cryptographic) smart cards for other purposes than establishing SSL.
You shall need additional code, executed by the browser, to access smart cards.
There are tens of custom and proprietary plugins (using all three options you mentioned) for various purposes (signing being the most popular, I guess) built because there is no standard or universally accepted way, at least in Europe and I 'm sure elsewhere as well.
Creating, distributing and maintaining your own shall be a blast, because browsers release every month or so and every new release changes sanboxing ir UI tricks, so you may need to adjust your code quite often.
And you probably would want to have GUI capabilities, at least for asking the permission of the user to access a card or some functionality on it.
For creating a multiple-platform, multiple browser plugin, something like firebreath could be used.
Personally, I don't believe that exposing PC/SC to the web is any good. PC/SC is by nature qute a low level protocol that when exposing this, you could as well expose block level access to your disk and hope that "applications on the web are mine only and they behave well" (this should answer your "Also"). At the same time a thin shim like SConnect is the easiest to create, for providing a javscript plugin.sendAPDU()-style code (or just wrap all the PC/SC API and let the javascript caller take care of the same level of details as in native PC/SC API use case).
Creating a plugin for this purpose is usually driven by acute current deficiencies.
Addressing the future (mobile etc) is another story, where things like W3C webcrypto and OpenMobile API will probably finally somehow create something that exposes client-side key containers to web applications. If your target with smart cards is cryptography, my suggestion is to avoid PC/SC and use platform services (CryptoAPI on Windows, Keychain on OSX, PKCS#11 on Linux)
Any kind of design has requirements. This all applies if you're thinking of using keys rather than arbitrary APDU-s. If your requirement is to send arbitrary APDU-s, do create a plugin and just go with it.
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