It depends on custom indicators and also how they are used. Normally indicators should be fast, but I saw some slow custom indicators. Maybe their code is not optimized. Custom indicator is written well when it calculates it's value only for the last candle on every tick. Bad written custom indicator is when it recalculates all candles on every tick.
In EA, use the custom indicator when needed. For example, if the EA needs to know the value from custom indicator only once when the new candle is created, put "Once per bar" before the condition, so that the condition will be executed once per bar and the indicator inside as well.
Also, if you have to check multiple indicators in a row, put the fastest at the top, or the one that can make the condition to pass not so often.