The problem is that the clipboard format that both Excel and Numbers can use to interchange data is very weak (this is a guess, I don't have access to Excel for Mac right now to verify, but it is almost certainly the case). This format is basically tab delimited text; no formatting, no cell properties or the like carries over on a copy from one into a paste on the other, just textual values. Copy and paste of the hidden property of the rows in Excel isn't going to happen.
I think to migrate this data from Excel to Numbers you'll need to do something rather heavy handed. Perhaps there is a column (or one could be added to the Excel sheet temporarily) that would have, say, 1's for shown rows and 0's for hidden. (Maybe it possible for an Excel whiz here on the forum can concoct a formula that computes this). Then, with all rows shown in Excel, select the new column and the other data and copy and paste into Numbers. Now in Numbers, you'll want to re-establish the hidden rows. This can be done superficially by filtering the rows using "Sort & Filter". If this "light weight" hiding is not desirable, perhaps someone else on the forum can think of a way to actually hide the rows based on the 1's and 0's column. I tried a couple of things but failed.
