I starting using separate compiled code from LV2010 when it first came out and am still doing so in LV2014. I have never had any problems with this feature, to the contrary it totally changed my option of LabVIEW and how it has become a 'real' programming language that is usable in a team development environment using proper source control tools.
I admit I have only been using it on Windows based platforms and though the projects have been big in number of VI's they have been quite simplistic compared to what a lot of you guys do.