In terms of farming, they make it harder to gather for yourself and they ruin the economy for crafted goods, like furniture.

Because they gather mats with no effort on the player's part, the botting player is often prepared to sell the items s/he makes, from those mats, for only a little more than the mat cost (sometimes even less!)

As opposed to the player who doesn't bot, who will want a decent mark-up, as they had to spend a long time tediously farming the mats needed and/or traipsing around the guild traders, trying (and often failing) to find decently priced mats.

In theory, they up the supply and lower the price of the mats; which should be good for the crafter.

However, in practice, because there doesn't seem to be that many of them who sell their raw furnishing mats in the game (I assume they're all selling any excess furnishing mats for real money on their websites), they don't even seem to do that.

Meaning furnishing mats in guild stores are still overpriced and rare, while crafted goods (like furniture) are often priced way too low (relative to the average available mat price).

It's the worst of all worlds...

...and in terms of things like PVP, in games in general, the presence of bots is almost always a complete disaster, for pretty obvious reasons.