THE PLT RCVD SVRL WX BRIEFINGS BFR TKOF & WAS ADZD OF CONVECTIVE ACTIVITY ALONG THE INITIAL ROUTE OF FLT NORTH OF THE ARPT. THE PLANNED DEP ROUTE WAS TWD THE WX. WHILE DISCUSSING ALTN ROUTING POSSIBILITIES, THE PLT INDCD HE WOULD ASK ATC FOR DEVIATION ARND THE WX AFTER TKOF. AFTER TKOF, HE CTCD HOUSTON ARTCC & RPRTD CLMBG TO 4000'. THE CTLR (WHO HAD JUST COME ON DUTY) WASN'T EXPECTING THE ACFT & DIDN'T SEE A FLT PROGRESS SLIP FOR N5568D. A DISCUSSION FLWD CONCERNING THE STATUS OF THE FLT PLAN WITH THE CTLR FINALLY CLRG N5568D TO MAINT 4000'. SOON THEREAFTER, RADIO CTC WAS LOST & THE ACFT CRASHED IN WATER (LAGUNA MADRE) ABT 8 MI NORTH OF THE ARPT IN AN AREA OF TSTMS & LOW OVC. THERE WAS EVIDENCE THE ACFT CRASHED IN ABOUT A 10 DEG NOSE DWN ATTITUDE. NO PREIMPACT PART FAILURE OR MALFUNCTION WAS FND. THE RELIEVED ARTCC CTLR SAID HE ADZD THE RELIEVING CTLR THAT N5568D HAD A CLNC, BUT HADN'T RPRTD AIRBORNE. THE RELIEVING CTLR SAID HIS VIEW OF THE FLT PROGRESS SLIP WAS BLOCKED & HE DIDN'T SEE THE SLIP UNTIL 1 MIN LTR. THE PLT HADN'T LOGGED ANY RECENT INST APCHS.