IMHO if they have chairs in the LYS, they won't care if you sit and knit a bit! But, why not ask them if they mind? They should welcome your presence, and they would then look forward to your business in the future!
One thing I try NOT to do while sitting in my LYS: I don't discuss with other knitters about places to get yarn cheaper than the shop!
The shop clerks can hear everything...and I'm sure they would cringe if they heard me telling their customers about other places to buy yarn!
THAT would be poor etiquette!