Is there a way to check how many messages are in a MSMQ Queue?

You can read the Performance Counter value for the queue directly from .NET:

using System.Diagnostics;

// ...
var queueCounter = new PerformanceCounter(
    "MSMQ Queue", 
    "Messages in Queue", 
    @"machinename\private$\testqueue2");

Console.WriteLine( "Queue contains {0} messages", 
    queueCounter.NextValue().ToString());