The effects in Reason would perform exactly the same pre and post recording. Adding Neptune to your incoming signal would also delay it significantly so monitoring becomes really really difficult. If you want to commit to the effect you use you can bounce that mixer channel with the added effects included. The hissy noise is a problem which Reason wouldn't be able to avoid at all because it's not causing that problem. It's probably your interface, pre gain set too high or just noisy pre's.
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