You can connect one Shopify store to each campaign in HypeAuditor. However, you can connect as many different Shopify stores as you need across all your campaigns.
Thus, there is no limitation on the amount of Shopify stores you can connect. The only limit you might have is the amount of active campaigns you can have on your account at one time; this limit is applied by your subscription plan.
In other words, the amount of Shopify stores you can connect to HypeAuditor Campaigns tool is equal the amount of campaigns you can create according to your individual plan.