No, they don't seem to have fully planned it out already.

First of all, it is not too natural for a TV show to plan out its entire run, especially if it is of largley episodic nature. While Arrow has certain season-spanning storylines, the seasons themselves are still largely self-contained and closed. It is not a show with a predetermined storyline, like Game of Thrones, so you wouldn't want to plan out its entire season schedule beforehand but rather aim for adaptability to viewer preferences and other developments, like e.g. the spin-off of The Flash which got then repeatedly integrated into the season 3 storyline.

Those are largely general concerns. But if we look at the flashbacks in particular, we can see that they are also quite self-contained and closed per season and, as you realized yourself, often feature new developments that haven't been hinted at before at all, from Sara's survival of the shipwrecking, to Oliver's visit to Starling City. Likewise their storylines often are constructed to support the present-day storyline, from Sara's appearance and involvement on Lyan Yu to Det. Lance's past alcoholism and conflicts with his daughter paralleling his present conflicts.

And last but not least, a recent interview with co-showrunner Mark Guggenheim about the plans for season 4 reinforces the above points and shows that the writing decisions for the flashbacks in the new season were driven by impressions from the previous season:

FLASHBACK TO BASICS | On the issue of flashbacks — TVLine had pointed out that Oliver’s Hong Kong escapades weren’t nearly as compelling as his island or freighter adventures, nor did they strongly synch up with the present-day arc — Guggenheim met us halfway. “I’ll be honest: The episodic connection, week to week… that cart started to drag the horse for me a bit,” he admitted. “So toward the end of last year I said to the writers, ‘What we really need to do is not worry so much about the connection between present and past and just tell a really amazing story in the past.'” As a result, the Season 4 flashbacks, which kick off in Coast City but then head to a destination being kept under wraps, have Guggenheim “really happy.” As he raved, “I feel like we have our best flashback story ever.”

And in another interview he explains how Ollie's past love story is explictly constructed as a contrast to his present one (developed in season 3), which doesn't sound like any of that was pre-planned at all.

Though, the show itself is also very different. Guggenheim continues, “Because we’re going lighter in tone in present day, we’re going darker in flashbacks. This isn’t going to be a fun, rollicking romance in the past. But it does exist to contrast what’s going on in the present.” He adds, “The truth is, had Oliver and Felicity not gotten together in the present, I don’t know if we would have thought to give Oliver a love interest in the past.”

At least according to Stephen Amell, the writers did have "a plan" for Oliver's timeline during the five years he was missing. He gave an interview with ComicBookMovie early on in Season 2, where he claimed:

Oliver has a back story… and we have a plan to tell that backstory over 5 seasons.

This doesn't mean they have the entire 5 seasons worth of flashbacks scripted out. They only write and film a handful of episodes in advance, so their five-year-plan is most likely an outline of the basic details: where he is, what he's doing, etc. As Amell says in that same interview:

That’s the plan but all you ever think about is shooting episode 18 right now.

It's clear that at least some aspects of his island story are being written on the fly; for example, the entire storyline involving Constantine could not have been planned out until Constantine aired and was cancelled.

But the producers started the show with Oliver on the island, but dropped hints across Season 1 that he did other things (somehow joined the Russian mob, somehow met Amanda Waller, etc.) These big-picture items are probably part of their five-year plan, with the details being fleshed out as the shows get written.