Actually, here's a fix from the amazing Schwartz Edmisten:
//Shrink Your Logo
.header-announcement-bar-wrapper .header-title-logo img {
transition: max-height 140ms ease-in-out
}
.header-announcement-bar-wrapper.shrink {
padding-top: 20px!important;
padding-bottom: 20px!important;
.header-title-logo img {
max-height: 40px;
}
}
Source: https://schwartz-edmisten.com/blog/shrink-logo-on-scroll-in-squarespace-71