It does not mean limited time per say, Legacy used to refer to older skins that were not up to modern standards, but over time it also evolved into event skins. Basically if a skin is a legacy skin it usually means you cant buy it in the shop all the time, but they will go on sale in the shop during events or other stuff (Ie snowdays stuff around Christmas). Now some Skins off course are rarer and don't pop into the Store (Judgement Kayle), but most legacy will show up eventually or semi frequently. Now to your actual point, while unable to be gained in the store most legacy skins can still be dropped in the hextech chests even when not in the store.
TL:DR Legacy usually just means skins that are not available in the store all the time. Despite this most of these skins can still be dropped through Hextech chests at any time.