The whole point of SMTs (as far as I understand) is to use them on sites other than SteemIt.com. SteemIt is really just the first proof of concept site for the Steem blockchain. If it remains the primary front-end for Steem then I think Steem and SMTs will have failed.

If each SMT has their own front-end site, then sure - one or a few of them could be DDOSed, but it wouldn't be all that big of a deal since there will ideally be so many different sites running on Steem.

Overall I think the fact that the majority of people still use SteemIt.com as their only interface to Steem (and that many people don't know the difference between the two) is one of the biggest problems facing the platform right now. The DDOS the other day may have been a very good thing in that it spurred so many posts and so much learning about how the system works and that SteemIt.com is only a front-end website.