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That will definitely work. It is tough stuff to get off if you make a mistake. For baffles you’re fine with silicone sine there’s very little pressure.

Have you gotten the acrylic baffles cut yet?
 
I've used silicone to do acrylic, you just sand the edges and understand you're making more of a gasket than a straight bond. Just make sure your acrylic baffles are not set in tight as acrylic will expand and you could shatter the glass tank. That said give E6000 a shot, I think I've seen it at big box stores (lowes, HD) in the adhesive section so it should be easy to test out.
 
I was asking for the same reason @sfsuphysics mentioned. You’ll want to cut them a bit smaller (I’d say 1/8”) than the width of the opening that they’re spanning since acrylic does absorb some water and will expand slightly.
 
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