Does isolation have any effect upon mouse behavior?
Yeah, it's not good:


  Social isolation (SI) rearing in rodents causes a variety of behavioral changes, including hyperlocomotion, anxiety, impulsivity, aggression, and learning and memory deficits. These behavioral abnormalities in rodents may be related to the symptoms in patients with neuropsychiatric disorders, such as attention-deficit hyperactivity disorder, obsessive-compulsive disorder, autism, schizophrenia and depression...


Also:


  Our findings suggest that [social isolation]-induced behavioral abnormality is a psychobehavioral complex relevant to various clinical symptoms observed in neuropsychiatric disorders, including ADHD, schizophrenia and depression, and that SI-reared mice are a useful animal model to study the pathophysiology/pathogenesis of these diseases.


There's this:


  In contrast, long-term social isolation is a model to study the behavioral and neurochemical consequences of depriving rodents of social interaction. Many of the symptoms caused by long-term isolation resemble those seen in depression and anxiety disorders. Furthermore, long-term isolation of male mice is known to induce offensive and aggressive behavior, such as attacks.


And this:


  These data suggest that long-term isolation may induce functional changes in the sensitivity of alpha 2 receptor in the noradrenergic system...


And this:


  In the present study, we found that social isolation elevated the anxiety levels of mice...


Emphasis all my own.

There's a lot more meat in those studies, and especially the paper they cite in their introductions.  Some of them, as well as others also explore the effect of isolation in addition to other substances.  It can absolutely affect your studies, in particular behavioral or expression-based studies.  Your mouse house is good to change their practices.