Layers of liquid with glittered glue and shredded hot glue stick in a test tube
Yes, it's likely that an off-the-shelf glitter glue will give out, if it hardens at all in the wet environment. Glitter glue is a PVA glue, which tends to soften and dissolve when exposed to water; it's the same base as "washable school glue," and while different PVA glues have different solubilities, the base used in glitter glues is a highly soluble base for easy clean-up when used by children. "Shredded hot glue" is not going to provide a sufficient moisture barrier to prevent the glue from eventually being dissolved away by the water, and it's unlikely that the PVA glue will sufficiently bond to the glass to stop liquid from seeping between layers, especially as it begins to dissolve.

You may wish to use a different type of glue, but as an alternate approach, evaluate what appearance you want from this at the end. Is it just layers of translucent colors? If so, consider tinted crafting resins (please follow all safety instructions!); these will be solid when they cure, and will have no risk of spilling or mingling with each other. If the liquid appearance is important, use a waterproof glue that will also adhere to glass, such as aquarium glue, but be aware that this may not dry when in direct or near-direct contact with the liquid. You'll want to test it before committing to your full project.