Sorry this is so long, but it's important, and I didn't want to give your question an overly simplistic answer...
Pertaining to the Zenith 601/650 (virtually identical airplanes structurally), AOPA published a blog article that you might want to read before deciding to fly an un-modified one "as is"... Here's a link to the article:
AOPA Blog. Be sure you follow the link in that article to the FAA's Special Airworthiness Information Bulletin on that topic and read it as well. It's rather eye-opening! The key finding (for me at least) was that the designer did not meet the ASTM design standards when it came to wing loading. The FAA found issues with flutter, stick force gradients, airspeed calibration, and with the operating limitations.
So, you asked whether "
the failures that have happened [were] due to bad building, design or overstressing the aircraft?" The "root cause" appears to have been poor design, which was then amplified because pilots were inadvertently (and perhaps sometimes knowingly?) overstressing the airplane. Some of this was caused by the stick force gradient problem, potentially compounded by flying very close to the published limitations of the airframe. Though some were likely caused by the pilot flat-out ignoring the limits because "pilot excuse"... (I can fly aerobatics in this airplane – I'm just that good!)
The FAA felt (and Zenair agreed) that the fixes and new operating limitations are mandatory, but neither has the authority to enforce those for experimental aircraft under the current rules. So, while most owner/operators either fixed their 601/650s per the Zenith repair kits (though a few simply scrapped the airplanes out of an abundance of caution), some chose to ignore the waving red flags, and continued to fly the planes unmodified. Worse yet, some of the pawn these unmodified (and flat-out
dangerous, in my opinion) airplanes off on others – buyers who sometimes don't have the knowledge and experience to look beyond the shiny paint and pristine interiors to learn the background on these planes before buying one, flying it, and possibly killing themselves when it comes apart in the air.
You also asked "
If i purchase one without the mods that has a few hundred hours on it..why would it all of a sudden not be safe?" It would NOT "all of a sudden" be unsafe. It is already unsafe NOW, according to both the FAA and to Zenair (the designer / kit manufacturer / S-LSA builder). You would literally be flying a ticking time bomb... A gust of wind, too much aileron, or who knows what could be the trigger to initiate flutter, causing the wings to fail and the plane to come apart in the air. (Does that sound alarmist? It isn't - it's basically taken from one of several NTSB reports on these events...)
Zenair developed a comprehensive fix, which includes a fairly major alteration to the wing structure, adding weights to balance the ailerons, and a few other items I cannot recall at the moment. I believe new operating limitations also emerged from that process. Once the Zenair modifications are applied, the airplane appears to be an excellent one. There has not been a single in-flight breakup on one that was modified per the kit. So, while I personally would absolutely
not fly in an unmodified CH-601 or CH-650, I would not hesitate to fly in one that has had the mods properly applied. I'd want to see logbook entries referencing the Zenair kit, instructions, etc. as confirmation, then I'd want to visually inspect the plane to see (as best I could) the mods in place. But if all that is OK, yeah, I'd fly it! By all accounts, they are safe, nice flying airplanes.
The "catch" is that while this modification became mandatory for S-LSA versions, it remained "optional" for E-LSA and EAB versions, based on the FARs... (Although the FAA did point out in that SAIB that Part 91.7 requires the PIC to determine if the airplane is in a condition for safe flight – implying that without the "fix" that would not be the case.) So if the owner of the plane you're considering can't show evidence that the airplane has been "fixed" and tries to tell you that it's perfectly safe without the modifications, don't just walk away, but
run!
If you like the 601/650 design, you might also want to consider the RANS S-19 Ventarra. It is also a low wing side-by-side design with excellent flying characteristics. People often confuse the two airplanes, although there are some differences if you look closely. There are fewer S-19s out there, but there's a nice one listed on the rans.com website, in the "Pre-Owned RANS" section.