As the others pointed out there is no limit on number of units in storage other then the total amount all you planets, ships and bases can carry.
Perfect example of this.
I'm currently playing a single player game in which one of the ai has over 40k units. Most of them are troops on planets(I've captured quite a few planets with 50+ troops).
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I hear voices in my head... and they're not the ones I normally hear.
When you reach either the maximum number of ships or units, the message is also accompanied by a picture with a red 'target' circle with a picture of a generic ship or unit.