Hi there. Zyra's W gives CDR for two reasons:
First, Seeds have relatively little inherent value. We wanted to ensure that Zyra could cast more spells as she began to replenish her seeds faster, because as you put more points into W, you are expressing a desire to have more plants.
Second, because we wanted Zyra to be able to buy non-CDR items. We wanted players to be able to buy the items that made sense for them in their particular game from the entire line of mage oriented items, such as Zhonya's or Abyssal Scepter, not be restricted to the (at the time) small pool of CDR items.
A bit of context: We struggled during her development to balance 0% CDR Zyra builds against 40% CDR Zyra builds. The latter could put so many seeds out that certain enemy team compositions felt completely stifled. When W's cooldown was at a healthy level assuming 40% CDR builds, all other item paths felt terrible. Giving Zyra "free" CDR (20% on release) was accompanied by raising the cooldown of her W to compensate, meaning that Zyra's effective CDR cap for Rampant Growth was 20%.
Today, it's unlikely we would make the same decision, as CDR is a much more accessible stat. This is the reason that I lowered Zyra's passive CDR on W from 20% at max rank to 10%. In a game now filled with CDR choices, the "free" 20% was actually stifling her ability to purchase items. Hopefully getting to 40% these days involves a good amount of choice and compromise without leaving the player feeling like they are struggling to get to cap if they so desire or going way over if they do opt for CDR items.