1. Ideally, put your ships in low-power mode or similar so that they don't fire on the enemy until you want them to. Then get them into empty space on an AI planet. You can even bring in a conventional forces, if you wish, to draw away some of the AI forces and then go in for the kill with your stealth forces that the AI isn't aware of the position of.
2. You need to carefully use choke points to make best use of your tachyon units. Also, if you put the tachyon beams near the wormhole, you only need one per wormhole since that will give you some visibility into the AI presence on your planet and a limited window in which to engage them. You'll notice that's also mostly how the AI uses its own tachyon units.
In terms of why the low cap of anti-stealth units, think of it this way: supposing you could blanket your entire chain of plannets in tachyon beams. What would gameplay against a stealth AI then be like? It would be... the same as playing against a non-stealth AI opponent, right? Except that you'd be "taxed" in the form of building all those tachyon structures. That's boring, and just a hassle that leads you back to the same-old gameplay as long as you're willing to maintain your structures. Giving you a limit, however, means that playing against a stealth opponent is actually different.