Hi Tony.
I guess it depends on what the glass is and whether or not it has a reflection free coating on it. If it's a decent coating and decent glass you should lose no more than 1% of your light.
You could remove it, but I would advise caution, especially if the optics compartment is a sealed chamber. It's amazing how dust in the air is attracted to the internal mirrors, and if you're using it in either haze or fog... Well, let's just say that your mirrors will be crapped up in no time at all.
The only way for sure to test the losses through the exit aperture is to use a power meter, both before and after the glass. That way you'll be able to measure the losses exactly rather than guessing.
The Ophir heads that come up from time to time are a good buy as you can link them directly up to a voltmeter for the readout. Other than that there's 'Lasersbee' here on the forum that makes a nice solution.
If you're looking for a more 'commercial' solution i've seen the Laserwave power meters and they seem pretty good. Might be worth a quick email to Bridge to ask him for a price.
Cheers
Jem
Quote: "There is a theory which states that if ever, for any reason, anyone discovers what exactly the Universe is for and why it is here it will instantly disappear and be replaced by something even more bizarre and inexplicable. There is another that states that this has already happened.”... Douglas Adams 1952 - 2001