Just check all declarations, don't call isUncalledFunction

src/compiler/checker.ts

@@ -35323,7 +35323,7 @@ namespace ts {
                     error(node, Diagnostics.Re_exporting_a_type_when_the_isolatedModules_flag_is_provided_requires_using_export_type);
                 }
 
-                if (isImportSpecifier(node) && isUncalledFunctionReference(target.valueDeclaration, target)) {
+                if (isImportSpecifier(node) && every(target.declarations, d => !!(getCombinedNodeFlags(d) & NodeFlags.Deprecated))) {
                     errorOrSuggestion(/* isError */ false, node.name, Diagnostics._0_is_deprecated, symbol.escapedName as string);
                 }
             }

tests/cases/fourslash/jsdocDeprecated_suggestion9.ts

@@ -0,0 +1,11 @@
+///<reference path="fourslash.ts" />
+
+// @Filename: first.ts
+//// export class logger { }
+// @Filename: second.ts
+//// import { logger } from './first';
+//// new logger()
+
+goTo.file('second.ts')
+verify.noErrors()
+verify.getSuggestionDiagnostics([]);