Wheel covers are definitely legal, else a host of non-structural rim fairings would make a slew of aero wheels illegal. Think Stinger disc, for example, or any Jet rim, any carbon faired alum rimmed wheel, etc.
On the other hand, unless the promoters say it, many EMX TT rules require a rim under a certain height. In other words an 808 may not fly, or a 1080, but a 202 or 303 might be okay. I think the 1080 is illegal for UCI mass start use, at least it was, so a "road bike TT" at the Tour of PA meant the max height wheel for Zipp teams was an 808.
EMX TT is usually not the same as "road bike TT".
The promoter, if interested in an EMX TT, ought to specify max rim height and minimum spoke count. If it's just a road bike TT then really anything except aero bars goes.
__________________
"...during the Lance years, being fit became the No. 1 thing. Totally the only thing. It’s a big part of what we do, but fitness is not the only thing. There’s skills, there’s tactics … there’s all kinds of stuff..." Tim Johnson