All electronic components are susceptible to SEU's at some point. I suggest you read
www.altera.com/literature/wp/wp-01135-stxv-seu-mitigation.pdf and
www.altera.com/literature/wp/wp-01012.pdf In general, on the ground it's not a big deal, but in aircraft, and space, it's a significant concern. Flash based devices are more robust than ram based devices, so if you can fit the design in a flashed based CPLD, it would be less likely to have issues. (IE Max series)
If you need more functionality than a CPLD, Actel (Now MicroSemi) makes flashed based and fuse based fpgas. They are on the smaller scale, but some of the fuse based guys are certified for space applications.
Pete