Yaan pointed me to this 2012 paper by Mrsic et al. They tested the Y chromosomes of 1100 Croatian men, 220 for each of the five regions. This allowed me to recalculate the haplogroup frequencies more accurately. So far, the small studies by Pericic et al. (2005) and Battaglia et al. (2008) only totalled a bit over 200 samples. The new frequencies are based on 1325 samples for the three studies combined.
The frequencies did change considerably. They decreased for haplogroups T (-1%), I1 (-2.5%), I2a (-5%) and R1a (-5%), but increased for E1b1b (+4%), J2, (+2.5%), G2a (+1.5%), J1 (+1%), Q (+1%), N (+0.5%) and R1b (+0.5%).
The frequencies did change considerably. They decreased for haplogroups T (-1%), I1 (-2.5%), I2a (-5%) and R1a (-5%), but increased for E1b1b (+4%), J2, (+2.5%), G2a (+1.5%), J1 (+1%), Q (+1%), N (+0.5%) and R1b (+0.5%).