Uber-wide tables: Time to switch to Mongo?
1) Consider how this information will be used.  Will the owner want to try lots of ad hoc analysis and data exploration?  Does your potential data store have tools or connection libraries that allow this?  Will the user have to resort to writing Map and Reduce functions for every question posed?

2) Do you mean that the same question is on different questionaires and you're wondering if you should recognise they're the same in your data store design?  Yes, absolutely you should, whatever thechnology you end up with.

3) The DBMSs have column limits, too.  They may be larger, but they're not infinite.

4) Store your data as one row per answer.  There are several qustions here on quiz design. Here's one picked at random.  These will give you pointers and any detailed questions remaining will be good material for future DBA.SE posts.