I'm glad to see that you also don't think highly of Greater Manyshot; I was under the impression that there was something useful about it I was completely missing, because it looked pretty bad on paper to me too.
Yeah, it really just doesn't stack up to Rapid Shot in almost all situations. I can think of specific niche builds where Greater Manyshot is better, like a Raptoran (or other 0 ECL flying race) using flyby attack. Generally, it's bad, though.
Thanks for pointing out the Hand Crossbow Focus feat. That wouldn't save me a feat from getting Rapid Reload because spelltheifs don't have hand crossbow proficiency, but it would save me a feat if I replaced Rapid Shot with TWF (because Point Blank shot is useless if I'm sneak attacking from 60 feet away). The only issue with this is that then I couldn't take use the Concealed Ambush/Manyshot strategy because Manyshot requires Rapid Shot and Concealed Ambush requires you not to be making a full attack, but it seems like that isn't a very effective build anyway.
Don't waste a feat on proficieny, it's worse in every single way than a light crossbow, and you can also fire light crossbows in one hand as light weapons anyway. And both require a hand to reload, so hand crossbow offers nothing special if you're spending an extra feat on it. If you dipped rogue a few levels, then consider it, otherwise don't.
I think you should go for Rapid Shot over TWF. Some argue that TWF's reduced penalties only apply to melee attacks (a view I don't agree with, but your DM might). Also, a Rapid Shot Xbow user can use a shield for more AC, focus his gold on only one weapon to enhance, and ends up with the same amount of attacks as the guy with a xbow in each hand anyway. And...face facts, you WILL need Point Blank Shot. It's required for Precise Shot as well. There IS a +1 weapon enhancement in Magic Item Compendium called Precise to be treated as having the feat when using that weapon. But getting a +1 enhancement on two weapons (you can't take Rapid without PBS, remember?) gets atrociously expensive very fast. One possible solution, I will say is a skill trick from...DMG 2 I think. Look for it in crystalkeep's skills and actions pdf. If you have a party member with Precise Shot, you can learn the teamwork benefit so the rest of the group gains half the feat's benefit (-2 to fire into melee instead of -4) for no real cost. If your group make-up leaves that an option, look into it. One final point in favor of PBS: Maybe you won't be within 30 ft the
first round. But you'll only be taking 5 ft steps while full attacking, and most enemies will want to close that distance. So you will in fact frequently end up within 30 ft whether you want to or not.
If I found another way to get sneak attacks in could you get an extra attack for each crossbow with TWF and Rapid Shot? I doubt I could pull it off (that's 5 feats alone, not counting Crossbow Sniper or Precise Shot), but it would be nice getting enough attacks in with my medium BAB.
A spellcaster ally and/or Use Magic Device are your best bets. Grease, Blink, Greater Blink, Improved Invisibility, and some others all work well to deny your foe dex to AC. If you have a party Druid, the Blinding Spittle spell in Spell Compendium (level 2) offers a no-save blindness if he can make the difficult attack roll (touch attack at -4 is hard at early levels). All it takes is a round washing the eyes out to remove, but that's a round of SA you didn't have, and some monsters will either be too stupid or not have any water immediately available to do that. Just elaborating on that specific spell since no one mentioned it yet.
Something that's become pretty much automatic for any rogue build I do now is a Swordsage dip. I like to do it at levels 9 and 10 to get immediate access to level 3 maneuvers, but you can do it sooner if needed. The reason for 2 levels is that you really want Assassin's Stance (+2d6 sneak attack!), but you can only pick up a level 1 stance at Swordsage 1 (and there's plenty of good options). You can spend a feat on the stance, but I'd rather use my level 9 feat on Adaptive Style (to repeatedly spam some awesome maneuvers the same combat) or Shadow Blade (if I was making a melee or thrown weapon build; not applicable for you). The maneuvers themselves are useful. Cloak of Deception is a swift action for Greater Invisiblity until end of your turn, for example. I like the level 1 Distracting Ember for a swift action flanking buddy, it's worthwhile if you ever get into any melee at all. You could do the Unarmed Swordsage adaptation listed so that you have a melee attack to threaten with (unarmed strike) even with your hands full of crossbows, if necessary.
Oh, to answer your question...simple hiding is lost on the first attack, but before a foe has acted that combat or any other method that lets you retain sneak attack conditions does in fact let you full attack with it. And don't forget the simple Haste buff spell for an extra attack (and +1 to hit). One fun thing to do with an archer is to dip Barbarian for the
Whirling Frenzy ability, taking Extra Rage to get it 3/day (the level 2 Druid spell Blood Frenzy from Spell Compendium also works and is
extremely "wand friendly" if you need to do it yourself). Whirling lets you take a -2 to get an extra attack, similar to flurry of blows, but with ANY weapon!