1.You will have the chance to catch those 2 again. You will encounter them again later in the game.
2.Ho-oh is given to you.
3. Yes. You can do the tower at much as want.
4. It's up to you. Some use it on T-Tar, others Meta or another. My stratagy is to go through the tower and keep all your ultraballs. If you get lucky and it's a female, chuck the ultras at it. If you can't catch it, use the master. If you want a female but get a male. Turn off the game and retry the tower. You shouldn't catch the shawdow Pokemon for this reason. If catch them and restart it's a pain to get them again. I just saved my masterball and tossed ultras at the big two (Meta and T-Tar). Whatever you want to do.