Yes, Splunk can. You can use SEDCMD- to rewrite the events to remove the \x00 s, which by the time the data hits an indexer are already the text "\x00" - they're no longer the null byte.
On the search bar:
| rex mode=sed "s/\\\\x00//g"
Automatically at parsing ("indexing") time for any new data, in props.conf:
[yoursourcetype]
SEDCMD-remove_nulls = s/\\x00//g
LINE_BREAKER = ((?:[\r\n](?:\\x00)?)+)
Special LINE_BREAKER was added because Splunk was interpreting the null bytes between \r and \n (the two halves of the Windows newline, in the file I was working on) as additional lines and adding them to the event. It says use " (one newline character optionally followed by the text \ x 0 0) one or more times " as the breaker (thrown away) between events.
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