"Javascript numbers are....not the greatest or most reliable. Especially when we are dealing with a crypto-currency, you really want your numbers to be on point. Basically JS uses floating point which means some things get approximated and digits get lost in certain cases. Here's some further reading: Be careful with big numbers & Floating point appoximation. So, the fact that everything in Lisk (including Lisk itself) is in Javascript, it means there are potentially big number problems (both in terms of big numbers and big problems)."
I agree it is a downside however I'm not sure it is a real concerns. There are many workarounds to this issue and most javascript developpers that need big numbers know how to deal with it.