It is possible that the statistics have changed since a stored procedure was compiled and thus may be executing a less the optimal execution plan, thus it may run slower.

I dont see any disadvantages..

Disadvantages (which pale by comparison) include:

Declining portability of code because these are SQL Server specific commands;
Less powerful and flexible programming language as compared to front-end front-end interface languages;
Sub-par development environment, although with Visual Studio .NET, this facility has been enhanced.

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